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Top Rated Payroll Software with Shopify

Last updated: October 2026

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17 software options

Gusto logo

Gusto is the all-in-one HR platform for growing businesses.

With Gusto, you get modern HR features like effortless payroll, benefits, hiring, management resources—and more. Gusto is proud to serve more than 500,000 businesses in the US with a single trusted system, competitive compensation tools, and expert guidance to help you empower your team.

Read more about Gusto

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Deputy logo

Staff scheduling and attendance tracking solution

Deputy is an all-in-one employee scheduling, time & attendance, tasking and communication platform, with mobile apps which allow users to manage teams on the go.

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Reckon One logo

Accounting software made for every small business

Easy and affordable online accounting and payroll software for Australian small businesses. Plans start at just $24 per month.

Read more about Reckon One

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Thareja AI logo

AI Agents for 24/7 Sales + Support | No need to hire people

Thareja lets businesses build AI support and sales agents trained on their own data — deployed across web, email, WhatsApp, Slack, and more.

Read more about Thareja AI

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Reckon Payroll logo

Payroll software made for every Australian small business

Affordable payroll software made for Australian small businesses. Includes unlimited users and is backed by Australian-based support.

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OneHash CRM logo

World's 1st FaaS(FOSS+SaaS)

A 100% smart SaaS-based, Robust, Scalable, Economical, & Fully- Featured platform with CRM, ERP, HCM, Project Management, Helpdesk solution, sales automation solution with built-in integrations available at $99/month for Unlimited Users.

Read more about OneHash CRM

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Facturama logo

Your easiest way to issue SAT-compliant invoices.

Generate CFDI 4.0 payroll receipts quickly and securely. Facturama lets you manage employee data and issue SAT-valid payroll documents with full compliance and automation.

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Wiise logo

Scalable cloud ERP for growing ANZ businesses.

Wiise is a scalable cloud ERP built on Microsoft Business Central and localised for ANZ businesses with $2–50m in annual revenue in industries including wholesale, financial & professional services, manufacturing, distribution, transport & logistics and not-for-profit.

Contact us today: wiise.com

Read more about Wiise

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Acumatica Cloud ERP logo

Cloud-based enterprise resource planning software

Acumatica Cloud ERP simplifies payroll with Payroll Management, Tax Compliance, and W-2 Preparation. It offers an Employee Database, Self-Service Portal, and Direct Deposit for efficiency. Benefits Management and Vacation Tracking enhance HR, while reports provide key insights.

Read more about Acumatica Cloud ERP

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FreshBooks logo

Invoice and accounting software tailored to small businesses

FreshBooks is accounting software that helps small business perform accounting tasks, conduct invoicing, manage expenses, and more.

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QuickBooks Payroll logo

Small business payroll platform

QuickBooks Payroll is a cloud-based payroll solution for small businesses which offers automatic payroll tax calculations, integrated time tracking, same day direct deposit, real-time data updates, tax form preparation and filing, and an online employee portal to streamline the payroll process

Read more about QuickBooks Payroll

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Xero logo

Cloud-based accounting software for small businesses

Xero's payroll tool enables you to track employee payroll information, generate payslips and reports, automatically update the general ledger, and more.

Read more about Xero

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NetSuite logo

AI-powered cloud-based business management suite

NetSuite is an AI-powered cloud-based business management suite. It helps organizations streamline their operations and gain real-time insights into their performance. The suite caters to a range of industries such as manufacturing, retail, and professional services.

Read more about NetSuite

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QuickBooks Online logo

Accounting and business management software

QuickBooks Online is a complete payroll solution which allows users to manage all their financial data in one platform, with real-time dashboards and reports.

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MYOB Business logo

Online accounting & payroll for every business

Cloud based accounting software to automate all your payroll requirements, plus client management, tax and all your accounting needs.

Read more about MYOB Business

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Nompli logo
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Your smart tax copilot

Nompli is a tax management platform for businesses, entrepreneurs, accountants, and independent professionals across Latin America. It simplifies tax compliance with country-specific tax tools, calculators, fiscal document validation, regulatory updates, tax guides, and educational resources.

Read more about Nompli

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Payrollix logo
(0)

Read more about Payrollix

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