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Finding the best accounting software with payroll capabilities is vital for small businesses aiming to streamline their financial operations. With the right software, you can save time, reduce errors, and improve compliance, allowing you to focus on growth. However, with so many tools on the market, it can seem impossible to know where to start. 

Using my experience in payroll software, I tested and compared some of the best solutions available, making sure to focus on ease of use, scalability, affordability, and support features. In this guide, we explore the top accounting software that includes payroll functionality, tailored to meet the unique needs of small businesses.

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Best Accounting Software With Payroll for Small Businesses Summary

Tools Price
Zoho Books From $15/user/month (billed annually)
Wave From $14/user/month
Gusto From $40/month + $6/user/month
Kashflow From $14.50/user/month
ClearBooks From $8/user/month (billed annually)
MYOB Business From $7/user/month (billed annually)
AccountEdge From $20/user/month
Patriot From $17/month + $4/employee
ZipBooks From $15/user/month
Kashoo From $27/user/month (billed annually)
Compare Software Specs Side by Side

Compare Software Specs Side by Side

Use our comparison chart to review and evaluate software specs side-by-side.

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How to Choose Accounting Software With Payroll for Small Businesses

As you work through your own unique software selection process, keep the following points in mind:

  • Cost and Budget: The cost of accounting software and payroll providers varies significantly based on features plus the number of users. For small businesses, finding a balance between affordability and functionality is vital. 
  • Usability and Accessibility: Consider how many users need access to the software and whether you prefer a cloud-based system or desktop software. Cloud-based solutions offer remote access from any device with internet connectivity, which is beneficial for businesses with remote teams or mobile access needs. 
  • Integration Capabilities: Ensure the accounting software integrates seamlessly with your existing systems, such as sales tax platforms, shipping systems, and payroll applications. This integration helps avoid compatibility issues and reduces the risk of errors. 
  • Features and Functionality: Identify the specific features your business needs, such as invoicing, expense tracking, financial reporting, and payroll services. Some software, like QuickBooks, offers advanced features including payroll, estimate creation, and receipt organization for in-house teams. FreshBooks, on the other hand, is ideal for independent contractors, freelancers, or very small businesses due to its client-based pricing model and monthly fees.
  • Customer Support and Security: Evaluate the quality of customer support and the security measures in place to protect your financial data. Reliable customer support is essential for resolving issues, and strong security features are important for safeguarding sensitive information and avoiding liabilities.

Best Accounting Software With Payroll for Small Businesses Reviews

Here are my in-depth overviews of accounting software with payroll for small businesses, including the pros and cons, features, and best use cases for each tool.

Best for customizable accounting tools

  • 15-day free trial
  • From $15/user/month (billed annually)
Visit Website
Rating: 4.5/5

Zoho Books is an accounting software designed for small businesses. It’s best for customizable accounting tools, offering a range of features that can be tailored to specific business needs.

Why I picked Zoho Books: Zoho Books provides advanced flexibility and customization options, allowing users to tailor their accounting processes to fit their unique workflows and preferences. Additionally, its seamless integrations with other Zoho apps and third-party tools make it highly adaptable, while automation features help streamline everyday financial tasks, saving time and reducing errors.

Standout features & integrations:

Features include strong invoicing, expense tracking, and inventory management, all of which can be customized to suit different business needs.

Integrations include G Suite, Microsoft Office 365, Slack, PayPal, Stripe, Square, Shopify, Zoho CRM, Zoho Projects, and Zapier.

Pros and cons

Pros:

  • Multi-language invoicing
  • Customized workflows
  • Built-in client portal

Cons:

  • Lack of fixed asset management
  • Restricted offline access

Best for free accounting and payroll

  • 30-day free trial + free plan available
  • From $14/user/month
Visit Website
Rating: 4.4/5

Wave is a small business software that offers accounting and payroll services. It provides a user-friendly interface and a range of features to help companies manage their finances effectively.

Why I picked Wave: Wave stands out for its free, easy-to-use tools for managing invoices, expenses, and financial reporting. The software’s built-in payroll and invoicing features, combined with the lack of subscription fees for core accounting tools, make it ideal for small businesses with limited budgets.

Standout features & integrations:

Features include invoicing, payments, accounting, and payroll. Wave allows users to create and send professional invoices, accept online payments, and manage their accounting and payroll needs all in one place. The software also offers a smart dashboard that organizes income, expenses, payments, and invoices.

Integrations include PayPal, Shoeboxed, Etsy, Zapier, Google Sheets, Slack, HubSpot, Mailchimp, Stripe, and QuickBooks.

Pros and cons

Pros:

  • Comprehensive financial management
  • User-friendly interface
  • Free accounting tools

Cons:

  • Reports customization
  • Limited customer support

Best for integrated payroll and HR solutions

  • Free demo available
  • From $40/month + $6/user/month
Visit Website
Rating: 4.3/5

Gusto is an online, full-service payroll and HR solution offering a variety of products and features to help small businesses manage payroll, benefits, and HR needs. It’s best known for its integrated payroll and HR capabilities, making it an advanced tool for small businesses.

Why I picked Gusto: Gusto excels in integrating payroll and HR functionalities, which is essential for small businesses aiming to streamline operations. The software uniquely combines payroll processing with HR management tools, offering a seamless experience for managing employee benefits, compliance, and payroll in one platform.

Standout features & integrations:

Features include automated payroll processing, employee benefits management, and compliance support. Gusto also offers tools for hiring and onboarding, time tracking, and performance management.

Integrations include QuickBooks, Xero, FreshBooks, Expensify, Hubstaff, Clover, Homebase, When I Work, TSheets, and ZipBooks.

Pros and cons

Pros:

  • Employee benefits management
  • Automated payroll processing
  • Comprehensive HR tools

Cons:

  • Setup complexity
  • Limited customization options

Best for customizable and integrated financial management

  • 14-day free trial
  • From $14.50/user/month
Visit Website
Rating: 4.1/5

KashFlow is an accounting software with payroll designed for small businesses, offering customizable and integrated financial management tools. It simplifies complex financial tasks with features like invoicing, expense tracking, and payroll processing, making it an advanced solution for small business owners.

Why I picked KashFlow: KashFlow offers an intuitive interface that simplifies bookkeeping, invoicing, and expense tracking. Its cloud-based platform allows for easy access, and its payroll integration helps small businesses manage employee payments and tax obligations efficiently. Additionally, KashFlow is scalable and highly customizable, making it a flexible option as the business grows.

Standout features & integrations:

Features include VAT returns, invoicing, payments, payroll management, and reporting tools.

Integrations include PayPal, GoCardless, Stripe, Dropbox, Mailchimp, Receipt Bank, Amazon, eBay, Shopify, and WooCommerce.

Pros and cons

Pros:

  • Comprehensive payroll features
  • VAT compliant
  • In-depth reporting

Cons:

  • Steep learning curve for new users
  • Limited mobile functionality

Best for AI-powered bookkeeping

  • 30-day free trial
  • From $8/user/month (billed annually)
Visit Website
Rating: 4/5

ClearBooks is an accounting software designed for small businesses, offering AI-streamlined bookkeeping, professional invoicing, and flexible online payment options to help businesses get paid sooner. 

Why I picked ClearBooks: ClearBooks provides users with a unique AI-powered bookkeeping feature, which sets it apart from other accounting software. This advanced technology significantly reduces the time spent on financial admin tasks, allowing small business owners to focus on growth. Additionally, its cloud-based system ensures accessibility from anywhere, and it integrates with popular banks and payroll systems, providing a seamless financial management experience.

Standout features & integrations:

Features include AI-streamlined bookkeeping, professional invoicing, and flexible online payment options. 

Integrations include PayPal, GoCardless, Stripe, Xero, QuickBooks, Sage, FreeAgent, KashFlow, FreshBooks, and Zoho Books.

Pros and cons

Pros:

  • Flexible payment options
  • Professional invoicing
  • AI-powered bookkeeping

Cons:

  • No mobile app
  • Advanced features may be overwhelming

Best for scalable business solutions

  • 14-day free trial
  • From $7/user/month (billed annually)

MYOB Business is an advanced business software platform designed to support small and medium-sized businesses with various accounting and payroll needs. It excels in providing scalable business solutions, with features that expand alongside your business growth.

Why I picked MYOB Business: MYOB Business dedicates itself to scalability, which makes it stand out from other accounting software. The software is designed to grow with your business, providing a range of features that cater to both small startups and expanding enterprises. This flexibility ensures that businesses won't outgrow the software as they continue to expand.

Standout features & integrations:

Features include invoicing, tax payments and management, payroll, inventory management, and financial reporting. 

Integrations include Lightspeed, PayGlobal, MYOB Practice, Arrow, Cardigang, Multi Dwell Developments, Hegi Design House, Xero, QuickBooks, and Reckon.

Pros and cons

Pros:

  • Award-winning software
  • Comprehensive features
  • Scalable solutions

Cons:

  • Limited multi-currency support
  • Complex setup

Best for desktop accounting

  • 30-day free trial
  • From $20/user/month

AccountEdge is a powerful and easy-to-use desktop accounting software for small businesses on Mac or Windows. It excels in desktop accounting with strong on-premise capabilities and optional remote access.

Why I picked AccountEdge: AccountEdge provides a wide-variety of features tailored to small businesses, including sales, invoicing, payroll runs, accounting, and inventory. It stands out for its reliability as a desktop accounting platform, offering both Mac and Windows applications with optional remote cloud access through AccountEdge Connect. This makes it an excellent choice for businesses seeking the security of on-premise software with the flexibility of remote access.

Standout features & integrations:

Features include sales, invoicing, payroll, accounting, and inventory. AccountEdge also offers advanced data management and reporting capabilities.

Integrations include Shopify, BigCommerce, WooCommerce, Square, Stripe, PayPal, Mailchimp, G Suite, Microsoft Office, and Dropbox.

Pros and cons

Pros:

  • Optional remote access
  • Comprehensive feature set
  • Reliable desktop platform

Cons:

  • Steep learning curve
  • Limited mobile app functionality

Best for affordability and value

  • 30-day free trial
  • From $17/month + $4/employee

Patriot offers affordable and easy-to-use accounting and payroll software for small businesses, providing advanced add-ons and features that streamline financial management. 

Why I picked Patriot: Patriot provides exceptional affordability and value, which stands out among other small business accounting software options. Its combination of low pricing and strong features makes it an excellent choice for small businesses aiming to manage their accounting and run payroll more efficiently. Additionally, Patriot's user-friendly interface and seamless integration of accounting and payroll functions further enhance its appeal.

Standout features & integrations:

Features include invoicing, tracking money, automatic payroll tax rate updates, and easy access to financial reports. Patriot's software is designed to be flexible and efficient, making it ideal for small businesses that need a reliable and cost-effective solution.

Integrations include QuickBooks, Gusto, Xero, Zoho Books, Kashoo, KashFlow, OnPay, AccountEdge, ClearBooks, and ZipBooks.

Pros and cons

Pros:

  • Mobile accessibility
  • Compliance with multi-state payroll
  • Customizable payroll reports

Cons:

  • Limited customization for invoicing
  • No inventory management integrations

Best for user-friendly interface

  • 30-day free trial + free plan available
  • From $15/user/month

ZipBooks is a free, online accounting software and invoicing platform designed for small businesses. It offers features such as accounting, billing, expense management, and intelligence, enabling users to send professional invoices, track expenses, and access smart insights and reports.

Why I picked ZipBooks: ZipBooks is known for its user-friendly interface, making it accessible even for those without an accounting background. Its simplicity and intuitive design make it an excellent choice for small business owners needing to manage their finances efficiently. The software helps teams streamline bookkeeping tasks, allowing users to focus on growing their business rather than getting bogged down by complex accounting processes.

Standout features & integrations:

Features include a complete accounting solution, one-time and recurring billing, smart expense tracking, and a full suite of reports and insights. ZipBooks also offers auto-categorization and intuitive color-coding to make bookkeeping straightforward.

Integrations include PayPal, Stripe, Square, Gusto, Slack, Google Drive, Google Sheets, Trello, and Asana.

Pros and cons

Pros:

  • Smart expense tracking
  • Efficient invoicing
  • User-friendly interface

Cons:

  • Steep learning curve
  • Limited advanced features

Best for simplicity and automation

  • 14-day free trial
  • From $27/user/month (billed annually)

Kashoo is an accounting software for small businesses, offering automated accounting, simplified invoicing, and easy expense tracking. 

Why I picked Kashoo: Kashoo offers a straightforward approach to accounting, standing out in a market filled with complex solutions. Its emphasis on automation and simplicity makes it particularly suitable for small business owners looking to save time and reduce manual accounting tasks. With a user-friendly interface and automated features, even those with minimal accounting knowledge can manage their finances effectively.

Standout features & integrations:

Features include automated income and expense tracking, simplified invoicing, and easy expense tracking and budgeting. Kashoo also offers detailed reporting and customization options, making it a versatile tool for growing businesses.

Integrations include Stripe, PayPal, Square, FreshBooks, QuickBooks, Xero, Gusto, HubSpot, Shopify, and WooCommerce.

Pros and cons

Pros:

  • Multi-currency support
  • User-friendly interface
  • Automated accounting

Cons:

  • Limited international support
  • Limited advanced features

Other Accounting Software With Payroll for Small Businesses

Below is a list of additional accounting software with payroll for small businesses that I shortlisted. While they didn’t make the top 10, they’re still valuable and worth further research.

  1. Xero

    Best for comprehensive accounting features

  2. ADP Workforce Now

    Best for comprehensive HR and online payroll features

  3. FreshBooks

    Best for user-friendly interface for small teams

  4. Unanet

    Best for project-based accounting and payroll

  5. Odoo

    Best for customization options for various industries

  6. Sage Accounting

    Best for scalability for growing businesses

  7. QuickBooks

    Best for integration with other financial tools

If you still haven't found what you're looking for here, check out these tools closely related to accounting software that we've tested and evaluated.

Accounting Software With Payroll for Small Businesses Selection Criteria

The criteria for choosing an accounting software with payroll for small businesses should directly address buyer needs and common pain points, ensuring that the software serves its intended purpose effectively. As an expert who has personally tried and researched these tools, here are the requirements I use when evaluating software:

Core Functionality (25% of Total Weighting Score):

  • Payroll processing and tax calculations
  • Financial reporting and analytics
  • Expense tracking and management
  • Invoicing and billing
  • Bank transactions and reconciliation

Additional Standout Features (25% of Total Weighting Score):

  • Integration with third-party apps
  • Mobile app functionality
  • Customizable dashboards
  • Advanced security features
  • AI-driven insights and automation

Usability (10% of Total Weighting Score):

  • Intuitive user interface
  • Drag-and-drop functionality
  • Role-based access control
  • Customizable workflows
  • Real-time collaboration features

Onboarding (10% of Total Weighting Score):

  • Availability of training videos
  • Interactive product tours
  • Pre-built templates
  • Chatbots for instant support
  • Webinars for in-depth training

Customer Support (10% of Total Weighting Score):

  • 24/7 availability
  • Multiple support channels (phone, email, chat)
  • Dedicated account managers
  • Comprehensive knowledge base
  • Fast response times

Value For Money (10% of Total Weighting Score):

  • Competitive pricing plans
  • Transparent pricing structure
  • Free trial availability
  • Discounts for annual subscriptions
  • Cost-benefit analysis

Customer Reviews (10% of Total Weighting Score):

  • Overall satisfaction ratings
  • Feedback on ease of use
  • Comments on customer support
  • Reviews on feature set
  • Testimonials on reliability and performance

Here are some trends I've observed in accounting software with payroll for small businesses and what they might indicate for the future. I analyzed numerous product updates, press releases, and release logs to extract the most significant insights.

  • Cloud-Based Solutions: Cloud-based payroll solutions are gaining popularity due to their flexibility and scalability. These platforms allow businesses to manage wages effortlessly, adapting to growth without significant infrastructure investment. The integration of compensation systems with other HR and accounting software ensures seamless data flow, reducing manual entry errors and saving valuable time.
  • Mobile Applications: The adoption of mobile applications for HR functions is accelerating. Mobile apps offer unprecedented flexibility for business owners and their teams, allowing them to manage payroll services on the go. This trend is supported by studies showing higher engagement rates with mobile applications compared to stationary web users.
  • Integrated Systems: Integrated payroll services are experiencing significant growth by providing comprehensive human capital management solutions on a single platform. This integration helps small businesses streamline operations, improve efficiency, and ensure compliance with evolving regulations.
  • Automation and AI: Artificial intelligence and machine learning are being incorporated into accounting software to automate routine tasks, improve data accuracy, and provide valuable insights for decision-making. AI-powered software can handle data entry, reconciliation, and simple financial analysis, freeing up time for more complex tasks.
  • Compliance and Security: Staying compliant with local and federal regulations is crucial for small businesses to avoid costly penalties. Accounting software with payroll features helps businesses stay updated with tax codes and employment laws. Additionally, strong cybersecurity measures are essential to protect sensitive employee information and build trust.

What Is Accounting Software With Payroll for Small Businesses?

Accounting software with payroll for small businesses helps manage financial transactions and payroll processes, enabling small business owners and accountants to track income and expenses, generate financial reports, and ensure timely and accurate employee payments. 

Typically, this software includes components such as a general ledger, accounts payable, accounts receivable, payroll processing, and tax compliance. These features allow users to maintain precise financial records, automate payroll calculations, and comply with tax regulations efficiently.

Features of Accounting Software With Payroll for Small Businesses

Choosing the right accounting software with payroll capabilities is vital for small businesses. It can streamline financial processes, ensure compliance, and save time. Here are some essential features to look for in such software:

  • Core Accounting Functions: Core accounting functions include recording transactions, managing the general ledger, and generating financial statements. These are essential for tracking revenue, expenses, and cash flow, ensuring the financial health of your business.
  • Payroll Management: Payroll management automates payroll calculations, tax withholdings, and benefits. It ensures timely and accurate payment to employees, which is vital for maintaining employee satisfaction and compliance with tax laws.
  • Budgeting and Forecasting: Budgeting and forecasting tools help businesses create financial plans based on historical and real-time data. This feature is important for tracking performance against budgets and making informed financial decisions.
  • Billing and Invoicing: Automated billing and invoicing streamline the process of generating invoices and tracking payments. This feature helps maintain cash flow and reduces the time spent on manual billing tasks.
  • Project Accounting: Project accounting allows businesses to track revenue and expenses on a project basis. This is particularly useful for businesses that undertake project-based work, ensuring accurate financial tracking and billing.
  • Asset Tracking: Asset tracking manages the value and details of long-term and short-term assets. This feature is essential for maintaining accurate records of asset values, depreciation, and inventory levels.
  • Reporting and Analytics: Advanced reporting and analytics provide real-time insights into financial performance. Customizable dashboards and reports help businesses monitor key metrics and make data-driven decisions.
  • Mobile Support: Mobile support allows access to financial data from anywhere, ensuring that employees can manage workflows on the go. This feature is particularly useful for businesses with remote or mobile workforces.
  • Tax Management: Tax management automates complex tax calculations and ensures compliance with local, national, and global tax requirements. This feature reduces the risk of errors and penalties associated with tax filings.
  • Integration: Integration with other business applications, such as ERP systems and CRM software, ensures seamless data flow across the organization. This feature enhances efficiency and reduces the likelihood of data-entry errors.

Benefits of Accounting Software With Payroll for Small Businesses

When choosing accounting software with payroll for small businesses, it's important to consider tools that can streamline operations, save time, and reduce errors. Integrated payroll functionality offers an advanced solution for managing finances and payroll efficiently. Here are a few of the primary benefits of using such software for small businesses:

  • Time Savings: Automating payroll processes reduces the time spent on manual calculations and data entry, allowing business owners to focus on other critical tasks.
  • Accuracy: The software minimizes human errors in payroll calculations, ensuring employees are paid correctly and on time, which helps maintain employee satisfaction and compliance with tax regulations.
  • Cost Efficiency: By reducing the need for external payroll services or additional staff, businesses can save money and allocate resources more effectively.
  • Compliance: The software helps ensure that payroll processes adhere to the latest tax laws and regulations, reducing the risk of costly penalties and audits.
  • Data Integration: Seamless integration with other accounting functions provides a holistic view of the business’s financial health, aiding in better decision-making and financial planning.

Investing in accounting software with payroll for small businesses can significantly enhance the efficiency and accuracy of financial operations. This not only saves time and money but also ensures compliance and provides valuable insights into the business's financial status.

Costs & Pricing of Accounting Software With Payroll for Small Businesses

When selecting accounting software with payroll for small businesses, it's essential to understand the different pricing plans and what each offers. Keep in mind that pricing can vary widely depending on the features and level of support you need. 

Below is a table outlining common plan types, their average prices, and the features typically included:

Plan Comparison Table for Accounting Software With Payroll for Small Businesses

Plan TypeAverage PriceCommon Features
Free Plan$0Basic income/expense tracking, invoicing, receipt generation, and limited user access
Personal Plan$10 - $50/monthIncome/exercise tracking, invoicing, financial reports, 1-2 user access, and basic payroll
Business Plan$50 - $150/ monthMulti-user access, recurring invoicing, expense reporting, inventory management, payroll processing, and mobile support
Enterprise Plan$150+/monthCustom fields, automated reporting, advanced budgeting, custom integrations, and international taxation handling
A breakdown of plan types, costs, and features for accounting software with payroll for small businesses.

Each plan caters to different needs, from basic financial management tools suitable for small businesses to comprehensive solutions designed for those with more complex requirements.

By carefully evaluating the features and costs of each plan, small business owners can select the accounting software with payroll that best aligns with their operational needs and budget, ensuring they are well-equipped to manage their finances effectively and efficiently.

Accounting Software With Payroll for Small Businesses FAQs

Here are some commonly asked questions about accounting software with payroll for small business:

How do I integrate my accounting software with my payroll system?

Integrating your accounting software with your payroll system typically involves using built-in integration features or third-party connectors. Most modern accounting software solutions offer direct integration with popular payroll services. You will need to follow the specific instructions provided by your software vendor, which usually involves setting up API keys or using pre-built connectors. Ensure that both systems are compatible and that you regularly sync data to avoid discrepancies.

What are the tax compliance features available in accounting software with payroll?

Accounting software with payroll often includes tax compliance features such as automatic tax calculations, electronic tax filing, and updates on tax law changes. These features help ensure that your payroll processes adhere to federal, state, and local tax regulations. Some software also provides alerts for upcoming tax deadlines and generates necessary tax forms like W-2s and 1099s.

How do I handle payroll for remote employees using accounting software?

Handling payroll for remote employees involves ensuring that your accounting software can manage multi-state payroll and comply with varying state tax laws. You will need to set up the correct tax jurisdictions for each remote employee and ensure that your software can handle different state tax withholdings. Additionally, consider using direct deposit features to streamline payments to remote employees.

Is it possible to manage employee benefits through accounting software with payroll?

Yes, many accounting software solutions with payroll capabilities allow you to manage employee benefits. This includes tracking health insurance, retirement plans, and other benefits. You can usually set up benefit plans within the software, assign them to employees, and manage contributions and deductions. Some software also integrates with benefits providers to streamline administration.

How secure is my payroll data in accounting software?

Payroll data security is a critical concern, and most reputable accounting software providers implement robust security measures. These measures typically include data encryption, secure user authentication, regular security audits, and compliance with data protection regulations like GDPR or CCPA. Always ensure that your software provider follows industry best practices for data security and consider additional measures like two-factor authentication.

What support options are available if I encounter issues with payroll in my accounting software?

Support options vary by software provider but typically include online resources like FAQs, user guides, and video tutorials. Many providers also offer customer support through email, phone, or live chat. Some may provide dedicated account managers or premium support plans for more personalized assistance. Check your software’s support section to understand the available options and response times.

What’s Next? 

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Simon Litt
By Simon Litt

Simon Litt is the editor of The CFO Club, specializing in covering a range of financial topics. His career has seen him focus on both personal and corporate finance for digital publications, public companies, and digital media brands across the globe.