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Top Rated Accounting Software with Shopify

Last updated: August 2026

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118 software options

NetSuite logo

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

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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A2X logo

Accurate ecommerce accounting, without the fuss.

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

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Refrens logo

One platform for invoicing, accounting, inventory and more

Refrens is an AI-powered finance and operations platform for invoicing, accounting, GST, expenses, payments, inventory, CRM and reporting. Use Refrens Eagle to scan bills, Trust Score to assess customers, and Refrens MCP to work with business data from ChatGPT or Claude.

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Link My Books logo

Accurate multi-channel ecommerce accounting, automated

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

Striven is a cloud-based, all-in-one business management ERP

Striven's accounting software connects invoicing, bank reconciliation, payroll, purchasing, and project activity to one general ledger, so transactions post automatically and your financials stay current, accurate, and audit-ready in real time.

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RepairDesk logo

Modern repair shop management software for repair shops.

RepairDesk is an all-in-one repair shop management software which provides repair ticketing, inventory, customer relationship management (CRM), invoicing, payment processing, marketing, reporting, and more. The cloud-based point of sale (POS) platform is perfect for all sorts of repair businesses.

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Syft Analytics logo

The interactive & collaborative financial reporting tool.

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

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OptimoRoute logo

Get routes that just work

OptimoRoute helps field service and delivery businesses provide stand-out service. The cloud-based software plans and optimizes routes in seconds. Save time and free up resources to grow your business. Get started with a 30-day free trial and scalable Starter, Business, and Enterprise pricing.

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Zenskar logo

Automation software for subscription & usage-based billing

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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Synder logo

Reconcile multichannel sales & recognize revenue with ease.

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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wJewel logo

Accounting, inventory, and invoicing for jewelry businesses

wJewel is a cloud-based solution that assists jewelry manufacturers, retailers, wholesalers, and refineries with managing accounting, inventory, and consignments. Key features include business analysis, purchase order management, invoice processing, data export, and label printing.

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Gestionale sul Web logo

Enterprise resource planning and accounting software

Gestionale sul Web is an ERP solution focused on accounting management, helping businesses handle billing, payments, financial flows, supplier orders, price lists, offers, sales documents, and margin analysis in one integrated platform.

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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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Holded logo

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

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

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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.

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Liberty REACT logo

Consignment and Resale Software

Liberty Consignment Software is a full-featured Cloud based Consignment and Resale Software used for Account and Inventory Management, Point of Sale transactions, Reports, and provides integrated options for eCommerce and integrated Credit Card processing.

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aACE logo

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

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

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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Bookkeep logo

Automated ecommerce and retail bookkeeping just got smarter.

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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POS Nation for Retail logo

Complete Point of Sale Solution to Streamline Your Business

POS Nation's retail point of sale supports retail businesses with a turnkey solution that includes software, hardware, support, and payment processing.

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FloristWare logo

Cloud-based POS software for retail florists

FloristWare is a POS solution for flower shops and florists that automates and streamlines business operations for better customer service

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Kentro logo

Modern ERP to streamline, automate and grow your Commerce!

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

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FreshBooks logo

Invoice and accounting software tailored to small businesses

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

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Versa Cloud ERP logo

Best ERP for Inventory Heavy Businesses

Has key accounting features for easy bookkeeping and financial reporting

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