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Top Rated Accounting Software with Shopify

Last updated: May 2026

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75 software options

NetSuite logo

NetSuite

AI-powered cloud-based business management suite

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NetSuite AI-powered accounting simplifies the process of recording transactions, managing AP and AR, and closing the books. NetSuite supports multiple currencies, languages, and compliance standards and ensures data is accessible securely worldwide.

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Xero logo

Xero

Cloud-based accounting software for small businesses

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Xero is an award-winning online accounting software designed for small business owners and accountants, available on any computer or mobile device with an internet connection. Automate your invoicing and reporting, get a full picture of your business with up-to-date financial data, and much more.

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Acumatica Cloud ERP logo

Acumatica Cloud ERP

Cloud-based enterprise resource planning software

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Acumatica simplifies accounting with tools for Accounts Payable, Receivable, Billing & Invoicing, and Bank Reconciliation. It streamlines Expense Tracking, Payroll Management, and Financial Reporting, while managing your General Ledger and Income & Balance Sheet effortlessly.

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Avalara logo

Avalara

Automated tax compliance for global businesses

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Avalara offers automated tax compliance software that simplifies sales tax reporting and filing for businesses of all sizes. Its agentic AI handles tax calculations, returns preparation, and exemption certificate management across jurisdictions.

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A2X logo

Accurate ecommerce accounting, without the fuss.

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A2X automates ecommerce accounting for Shopify, Amazon, Etsy, eBay, Walmart, and PayPal sellers. Trusted by ecommerce accountants worldwide.

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Refrens logo

Business operating system sales, accounting, and inventory.

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Accounting software for startups, service businesses, agencies, SMEs, manufacturers, and more.

Manage your billing, accounting, vendors, inventory, and sales in one place.

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Link My Books logo

Accurate multi-channel ecommerce accounting, automated

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Link My Books automates ecommerce accounting by turning payouts from all major sales channels into accurate, bank-matched entries in Xero or QuickBooks. Sales, fees, refunds, and taxes are clearly broken down, helping businesses maintain reliable, tax-ready financial records.

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Striven logo

Collaborative ERP for business process management

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Simplify your billing, purchasing, and collections while you run better, faster reports and get complete visibility into your financial operations.

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Syft Analytics logo

The interactive & collaborative financial reporting tool.

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Syft Analytics is the financial reporting and data analytics software that helps growing businesses understand their financial data.

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Zenskar logo

Automation software for subscription & usage-based billing

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Zenskar is a comprehensive billing software for SaaS companies, managing complex subscription and usage-based billing. It enables businesses to meter data and automate revenue accounting, analytics, and dunning. With its flexible contract builder and no-code usability, finance teams can configure any pricing model, from prepaid subscriptions with postpaid overages to custom discounts and entitlements, without needing engineering resources.

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Gestionale sul Web logo

Enterprise resource planning and accounting software

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Gestionale sul Web is an enterprise resource planning software that helps businesses of all sizes manage production, billing, orders, suppliers, and sales. Key features include automated supplier orders, order margin analysis, price lists management, payment processing, offers management, and financial flow tracking.

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Reckon One logo

All small and medium-sized businesses.

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Easy to use online accounting software for small businesses. Plans start at just $24 per month.

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Holded logo

ERP, Accounting, Invoicing & more for freelancers and SMBs.

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Manage your accounting with automatic movements from your documents and manual movements to complete your Balance sheet.

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aACE logo

Accounting, CRM, and ERP built for Medium-sized Businesses.

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aACE’s full-featured Accounting software integrates with our CRM and ERP modules to allow managers to track a sale from the lead to the balance sheet without duplicate data entry. Controllers can easily hop from a single entry in the GL to anywhere in the transaction chain.

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ERPAG logo

ERP for small and mid-sized companies

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ERPAG is a cloud-based ERP system for small and mid-sized companies, which covers sales, purchasing, inventory, production, payroll, business analysis, and more

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Synder logo

Reconcile multichannel sales & recognize revenue with ease.

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Synder helps SME and MidSize up sync, record and recognize online sales and subscriptions in QuickBooks, Sage Intacct or Xero. The platform ensures accurate reconciliation across multiple platforms and offers easy invoicing, transaction categorization and instant data analytics.

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Bookkeep logo

Automated ecommerce and retail bookkeeping just got smarter.

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Untangle the accounting and sales tax for your multi-channel ecommerce or retail business! Automatic, accrual-based daily sales and payment journal entries into QBO, Xero, Sage Intacct, or Zoho Books - for 60+ ecommerce platforms as well as retail, restaurant, and cannabis POS solutions!

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Kentro logo

Modern ERP to streamline, automate and grow your Commerce!

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Grow effortlessly and efficiently across single or multiple sales channels and marketplaces with Kentro.

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Versa Cloud ERP logo

Best ERP for Inventory Heavy Businesses

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Has key accounting features for easy bookkeeping and financial reporting

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FreshBooks logo

Invoice and accounting software tailored to small businesses

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FreshBooks automates daily accounting activities namely invoice creation, payment acceptance, expenses tracking, billable time tracking and financial reporting.

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ALERE logo

ERP software for businesses of all sizes

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ALERE is an enterprise resource planning (ERP) software that helps businesses in aviation, food and beverages, distribution, apparel, packaging, textile, and other industries handle operations related to order management, job scheduling, inventory tracking, dispatching, and other processes.

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Axonaut logo

All-in-one business management for small teams.

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Axonaut simplifies accounting for small businesses—manage expenses, invoices, payments, and financial reports in one secure, cloud-based platform.

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Docyt logo

Accounting automation software platform

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Docyt tames the chaos in your back office by collecting data and organizing it into actionable workflows, real-time business insights, and continuously updating and reconciling your accounting software.

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Xentral Software logo

Enterprise resource planning and inventory management tool

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Xentral Software is a cloud-based ERP system available with German and English-language interfaces. It helps businesses scale operations by automating backend processes. Key features include an API, CRM, sales orders, stock management, expense tracking, order processing, and billing & invoicing.

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SapphireOne logo

Enterprise Resource Planning software

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SapphireOne streamlines financial management with Accounts Receivable, Payable, and General Ledger, ensuring precise reporting and compliance. Real-time access and automation reduce errors, enhancing strategic decision-making. Its scalability and customisation support growth and boost productivity.

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