Best Payroll Software for Shopify
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Compare the Top Payroll Software that integrates with Shopify as of September 2025
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This a list of Payroll software that integrates with Shopify. Use the filters on the left to add additional filters for products that have integrations with Shopify. View the products that work with Shopify in the table below.
What is Payroll Software for Shopify?
Payroll software helps businesses automate the payment of salaries and wages to their employees. It is used to calculate and process payroll payments, manage employee information, and generate reports. It is a convenient and efficient way to ensure that employees are paid on time and accurately. Payroll software typically includes features for generating paychecks, direct deposit, tax filings, generating year-end tax forms (such as W-2s), and maintaining accurate payroll records. Additionally, many payroll software solutions integrate with time-tracking systems, HR management tools, and accounting software to simplify overall business operations and ensure accuracy in payroll processing. Compare and read user reviews of the best Payroll software for Shopify currently available using the table below. This list is updated regularly.
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1
FreshBooks
FreshBooks
Make invoicing and billing painless for your small business with FreshBooks. A top-rated invoice and accounting software for self-employed professionals and small businesses, FreshBooks offers a fast, easy, and secure way of crunching numbers so companies can focus on doing the work they love. It offers a wealth of powerful features that includes invoicing, expense tracking, time tracking, project management, payment processing, and reporting. FreshBooks also lets users work from anywhere with the Freshworks mobile app.Starting Price: $6.30/month -
2
Xero
Xero
Xero's payroll software, with its Gusto integration, makes payroll simple for small businesses. Automatically calculate taxes, file payroll taxes, and pay employees with ease, ensuring compliance with federal, state, and local regulations. Xero integrates directly with your account, syncing payroll data for accurate bookkeeping. With features like next-day direct deposit and automated filings, Xero streamlines payroll, saving you time and reducing administrative tasks.Starting Price: $20/month -
3
NolaPro
Noguska
NolaPro is a robust, Linux-based ERP for Accounting, Order Tracking, Inventory Management & Payroll, designed to rival much more expensive choices. It is fully customizable and scalable for any size business, unlike any accounting program available today. The Cloud version allows a "hands-off" approach, but can be downloaded on Linux or Windows platforms for those who prefer to have local control and security. Features include: Credit Card Processing, Fulfillment & Service Order, AP, AR, Inventory, CRM, General Ledger, Payroll, Timeclock, Client Payment Portal and integration with many 3rd party apps -- or request your own! NolaPro is multi-lingual, supports multi-currency, offers tons of options & add-ons, and comes fully loaded with over 150 standard reports. A+ reviews from TechRepublic, The Linux Journal, Entrepreneur Magazine and CNet agree that NolaPro provides flexibility, features and pricing which provide you unparalleled value in managing your business.Starting Price: $0 -
4
QuickBooks Online
Intuit
QuickBooks Online is the most popular accounting software in the world. QuickBooks Online makes accounting easy. Make tracking receipts, income, bank transactions, and more feel simple with the #1 small business accounting software. Snap photos of your receipts and link them to expenses right from your phone. Our agents are ready and available to answer all your QuickBooks questions. Use the apps you know and love to keep your business running smoothly. QuickBooks Online works on your PC, Mac, tablets, and phones. Click the link above to get a 30 day free trial and 50% off your first 3 months. More than accounting software. QuickBooks helps you track income, expenses, and stay ready for taxes. Customers find on average $3,534 in tax savings per year. Need more help? QuickBooks Live helps you stay organized and be ready for tax time. QuickBooks comes with a mobile app that help you run your business on the go—anytime, anywhere.Starting Price: $9/month (normally $15/month) -
5
Rippling
Rippling
Streamline your business with Rippling’s all-in-one platform for HR, IT, payroll, and spend management. Effortlessly manage the entire employee lifecycle, from hiring to benefits administration. Automate HR tasks, ensure compliance, and streamline approvals. Simplify IT with device management, software access, and compliance monitoring, all from one dashboard. Enjoy timely payroll, real-time financial visibility, and dynamic spend policies. Rippling empowers your business to save time, reduce costs, and enhance efficiency, allowing you to focus on growth. Experience the power of unified management with Rippling today. -
6
Razorpay
Razorpay
Power your finance, grow your business. Accept payments from customers. Automate payouts to vendors & employees. Never run out of working capital. Mix and match products from Razorpay's payment suite to solve for your exact business use case. With the easiest integration, completely online onboarding, feature filled checkout and best in class performance, quickly go live with Razorpay and experience the future of payments. Razorpay Payment Pages is the easiest way to accept payments with a custom-branded online store. Accept international and domestic payments with automated payment receipts. Take your store online instantly with zero coding. Preparation is everything! Use hosted Event Registration to quickly register event attendees online and send automated receipts. Raising money for a good cause? Our hosted Donations page saves you valuable time by automatically sending personalized 80G receipts. -
7
KashFlow
IRIS Software Group
Keep your accounts under control with KashFlow, an award-winning, cloud-based accounting software. Designed specifically for sole traders and growing businesses, KashFlow makes accounting painless and hassle-free by offering a jargon-free and feature-rich platform that is loved and used even by non-accountants. From quoting and invoicing, to payroll and reporting, KashFlow’s accounting software keeps it simple.Starting Price: $7.00/month/user -
8
MYOB
MYOB
MYOB Business is a comprehensive cloud-based accounting and business management software designed to streamline financial and operational processes for small to medium-sized enterprises (SMEs). It offers a wide range of features, including invoicing, expense tracking, payroll management, inventory control, and tax compliance. With real-time financial reporting and user-friendly dashboards, MYOB Business provides valuable insights to help business owners make informed decisions. The platform supports seamless integrations with banking systems, payment gateways, and other business tools, enabling automation and reducing manual tasks. MYOB Business is known for its scalability, catering to growing businesses by offering flexible pricing plans and customizable features to meet diverse industry needs.Starting Price: $11/month
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