Best Accounting Software for Ecommerce Stores

For most US Shopify stores, QuickBooks OnlineQuickBooks OnlinePayments and accountingQuickBooks Online is Intuit's cloud accounting software for small businesses. Free plan, paid from $38/mo, 30-day trial.Click for Scout's full analysis is the safest pick: Intuit builds its own Shopify Connector, it handles marketplace sales tax, and inventory tracking is there when you reach the Plus plan. XeroXeroPayments and accountingXero is cloud accounting software for small businesses, with invoicing, bill pay, bank reconciliation and reporting. Paid from $27/mo.Click for Scout's full analysis costs less, has no per-user fees and a free Shopify integration, but that integration does not account for US sales tax. Very small stores can start on WaveWavePayments and accountingWave is invoicing and bookkeeping software with a free Starter plan and a low-cost Pro plan. Free plan, paid from $19/mo.Click for Scout's full analysis for free, and FreshBooksFreshBooksPayments and accountingFreshBooks is invoicing and accounting software for small businesses and freelancers. Paid from $23/mo, 30-day trial.Click for Scout's full analysis is the pick only if your business runs mostly on invoices, such as wholesale.

Quick comparison

All prices are regular US monthly prices from each company's pricing page in November 2026. None of these four is listed as a Shopify App Store app in our data, so there are no App Store ratings to compare.

Our pick by store type

Brand-new or side-hustle store: WaveWavePayments and accountingWave is invoicing and bookkeeping software with a free Starter plan and a low-cost Pro plan. Free plan, paid from $19/mo.Click for Scout's full analysis Starter is free and gives you unlimited invoices, bills and bookkeeping records. You will enter or upload bank data by hand, since automatic bank import is a Pro feature. Wave does not describe a Shopify integration on its own pages, so plan on recording Shopify payouts yourself.

Growing US store with an accountant: QuickBooks OnlineQuickBooks OnlinePayments and accountingQuickBooks Online is Intuit's cloud accounting software for small businesses. Free plan, paid from $38/mo, 30-day trial.Click for Scout's full analysis. The Shopify Connector brings in sales, payouts, fees and customers, and it records Shopify-remitted marketplace taxes in Sales Tax Payable. Most stores will start on Simple Start or Essentials and move to Plus when they need inventory.

Store selling in several currencies, or a team watching costs: XeroXeroPayments and accountingXero is cloud accounting software for small businesses, with invoicing, bill pay, bank reconciliation and reporting. Paid from $27/mo.Click for Scout's full analysis. Its pricing page says there are no per-user license fees, multi-currency is on Established, and the Shopify integration is listed as free on all Xero plans.

Wholesale or B2B seller that sends invoices: FreshBooksFreshBooksPayments and accountingFreshBooks is invoicing and accounting software for small businesses and freelancers. Paid from $23/mo, 30-day trial.Click for Scout's full analysis. Its plans are built around invoices, estimates, proposals and retainers.

QuickBooks Online

QuickBooks OnlineQuickBooks OnlinePayments and accountingQuickBooks Online is Intuit's cloud accounting software for small businesses. Free plan, paid from $38/mo, 30-day trial.Click for Scout's full analysis is the default choice for US store owners who want full bookkeeping software their accountant already knows.

Pricing. QuickBooks' pricing page lists monthly prices, with no annual contract and cancel-anytime terms:

• Free: 1 user, 2 invoices a month, top 3 reports, 1 connected bank. Fine for trying it, not for running a store.
• Simple Start: $38/month, 1 user. Automated bookkeeping, invoicing with payments, free ACH bill pay.
• Essentials: $85/month, 3 users. Adds enhanced reports and quarterly tax estimates.
• Plus: $140/month, 5 users. Adds inventory tracking, budgeting, project profitability, classes and locations, and sales tax discrepancy checks.
• Advanced: $340/month, 25 users. Adds custom permissions, workflow automation, batch transactions and bill approval workflows.

New customers get 50% off for the first 3 months, and the page lists a 30-day free trial.

Shopify integration. Intuit's help center describes the Shopify Connector by QuickBooks, installed from the QuickBooks Apps store. According to that guide:

• You choose whether Shopify sales are recorded individually or as a summary.
• Shopify payouts are imported, and you can review each one or have them added automatically.
• Shopify fees post to an expense account you choose.
• Customers are imported, and products are matched to your Products and services list by name.
• Taxes Shopify remits as a marketplace go to Sales Tax Payable; taxes you are responsible for go on the sales receipt.
• Transactions usually show up for review within 2 hours of completing in Shopify.

The guide does not state a price for the connector or name a required plan.

Watch out: Inventory tracking starts on Plus at $140/month, which is a big jump from Essentials. Simple Start allows only one user.

Skip it if: you are a one-person store with a few orders a week. WaveWavePayments and accountingWave is invoicing and bookkeeping software with a free Starter plan and a low-cost Pro plan. Free plan, paid from $19/mo.Click for Scout's full analysis or XeroXeroPayments and accountingXero is cloud accounting software for small businesses, with invoicing, bill pay, bank reconciliation and reporting. Paid from $27/mo.Click for Scout's full analysis Early will cost less.

Xero

XeroXeroPayments and accountingXero is cloud accounting software for small businesses, with invoicing, bill pay, bank reconciliation and reporting. Paid from $27/mo.Click for Scout's full analysis is the stronger value pick, especially for teams, because you do not pay per user.

Pricing (US, monthly):

• Early: $27/month. Quotes, 20 invoices and 5 bills a month, bank reconciliation, 30-day cash flow forecast. Auto-reconcile is a $5/month add-on.
• Growing: $59/month. Invoices included, automated bill entry, auto-reconcile, 60-day forecast, 3 budgets. Inventory Plus is an optional add-on (price not listed).
• Established: $97/month. Adds multi-currency, projects, expense and mileage claims, 180-day forecast and international bill payments.

New US customers get 80% off the base plan for the first 3 months. Payroll, powered by Gusto, is $36/month plus $6 per employee or contractor.

Shopify integration. Xero's App Store lists the Shopify integration "By Xero," free on all Xero plans, with setup help from Amaka. It syncs sales from the Shopify online store and Shopify POS, matches payouts from Shopify Payments and other gateways to your bank account (handling fees, refunds and taxes), and records sales either as a daily summary or as individual sales with customer and product lines. You can pull in up to 90 days of history. It is rated 4.7 from 76 reviews, as listed on the Xero App Store in November 2026.

Watch out: Xero's own Shopify page says the integration "does not account for sales tax in the US," so you export sales tax data from Shopify for filing. Neither page mentions inventory sync. And Early's 20-invoice, 5-bill monthly cap is tight; Xero does not say on these pages whether synced Shopify sales count toward it, so check before choosing Early.

Skip it if: you are a US store that wants sales tax handled inside your books, or you need inventory without paying for an add-on whose price is not published.

For a deeper head-to-head, see QuickBooks vs Xero for ecommerce.

Wave

WaveWavePayments and accountingWave is invoicing and bookkeeping software with a free Starter plan and a low-cost Pro plan. Free plan, paid from $19/mo.Click for Scout's full analysis is the cheapest way to keep real books.

Pricing. Starter is free: unlimited estimates, invoices, bills and bookkeeping records, with manual bookkeeping. Pro is $19/month or $190/year, priced per business, and adds automatic bank import (via Plaid, where supported), auto-categorization, late payment reminders and user roles. Payroll starts at $25/month extra, and Wave Advisors bookkeeping starts at $149/month.

Card fees. If you take payments through Wave invoices, Starter pays 2.9% + $0.60 per Visa/Mastercard/Discover transaction (3.4% + $0.60 for Amex). Pro drops the $0.60 on the first 10 transactions each month. This matters for invoices, not for checkout on your Shopify store, which runs on Shopify's own payments.

Shopify integration. Wave's pricing page does not mention Shopify, ecommerce or inventory, and we did not find a Shopify integration described on Wave's own pages. Third-party connectors exist, but we have not reviewed them here.

Skip it if: you need inventory, multiple currencies, or an automatic Shopify sync. Move to QuickBooks OnlineQuickBooks OnlinePayments and accountingQuickBooks Online is Intuit's cloud accounting software for small businesses. Free plan, paid from $38/mo, 30-day trial.Click for Scout's full analysis or XeroXeroPayments and accountingXero is cloud accounting software for small businesses, with invoicing, bill pay, bank reconciliation and reporting. Paid from $27/mo.Click for Scout's full analysis.

FreshBooks

FreshBooksFreshBooksPayments and accountingFreshBooks is invoicing and accounting software for small businesses and freelancers. Paid from $23/mo, 30-day trial.Click for Scout's full analysis is invoicing software first. It is a good fit for stores with a wholesale or custom-order side, and a weak fit for a pure direct-to-consumer Shopify store.

Pricing (monthly):

• Lite: $23/month, 5 billable clients. Invoices, estimates, expense tracking, card/ACH/Apple Pay/Google Pay payments.
• Plus: $43/month, 50 billable clients. Adds bank reconciliation, double-entry accounting reports, receipt scanning and accountant access.
• Premium: $70/month, unlimited clients. Adds accounts payable and project profitability.
• Select: custom pricing.

Extra team members are $11/month each. Advanced Payments is $20/month on Lite, Plus and Premium. Payroll is $40/month plus $6 per user. The current offer is 80% off for 4 months, there is a 30-day free trial with no card needed, and the yearly option is labeled "Extra 10% Off" (yearly prices are not shown).

Shopify integration. FreshBooks' pricing page does not mention Shopify, ecommerce or inventory, and we did not find a FreshBooks-built Shopify integration on its own pages.

Skip it if: your revenue comes through a Shopify checkout rather than invoices. You would be paying for invoice tools you won't use, and bank reconciliation does not start until Plus.

What it costs at two store sizes

These use only the published prices above, at regular rates (before intro offers).

Solo owner, under 100 orders a month, no inventory tracking:

• WaveWavePayments and accountingWave is invoicing and bookkeeping software with a free Starter plan and a low-cost Pro plan. Free plan, paid from $19/mo.Click for Scout's full analysis Starter: $0. Pro: $19/month, or $190/year (about $15.83/month).
• XeroXeroPayments and accountingXero is cloud accounting software for small businesses, with invoicing, bill pay, bank reconciliation and reporting. Paid from $27/mo.Click for Scout's full analysis Early: $27/month, if the 20-invoice and 5-bill limits fit your setup.
• QuickBooks OnlineQuickBooks OnlinePayments and accountingQuickBooks Online is Intuit's cloud accounting software for small businesses. Free plan, paid from $38/mo, 30-day trial.Click for Scout's full analysis Simple Start: $38/month.
• FreshBooksFreshBooksPayments and accountingFreshBooks is invoicing and accounting software for small businesses and freelancers. Paid from $23/mo, 30-day trial.Click for Scout's full analysis Lite: $23/month, but bank reconciliation needs Plus at $43/month.

Three-person team tracking inventory:

• QuickBooks OnlineQuickBooks OnlinePayments and accountingQuickBooks Online is Intuit's cloud accounting software for small businesses. Free plan, paid from $38/mo, 30-day trial.Click for Scout's full analysis Plus: $140/month, covers 5 users and inventory.
• XeroXeroPayments and accountingXero is cloud accounting software for small businesses, with invoicing, bill pay, bank reconciliation and reporting. Paid from $27/mo.Click for Scout's full analysis Growing: $59/month plus Inventory Plus, whose price Xero does not publish. No per-user fees.
• FreshBooksFreshBooksPayments and accountingFreshBooks is invoicing and accounting software for small businesses and freelancers. Paid from $23/mo, 30-day trial.Click for Scout's full analysis Premium with two extra team members: $70 + $22 = $92/month, but no inventory tracking is listed.
• WaveWavePayments and accountingWave is invoicing and bookkeeping software with a free Starter plan and a low-cost Pro plan. Free plan, paid from $19/mo.Click for Scout's full analysis: no inventory feature listed.

Which one should you choose?

• Choose QuickBooks OnlineQuickBooks OnlinePayments and accountingQuickBooks Online is Intuit's cloud accounting software for small businesses. Free plan, paid from $38/mo, 30-day trial.Click for Scout's full analysis if you sell in the US, want sales tax and Shopify payouts handled in your books, and expect to need inventory later.
• Choose XeroXeroPayments and accountingXero is cloud accounting software for small businesses, with invoicing, bill pay, bank reconciliation and reporting. Paid from $27/mo.Click for Scout's full analysis if you want lower monthly cost, several users without per-seat fees, or multi-currency, and you are fine handling US sales tax from Shopify's reports.
• Choose WaveWavePayments and accountingWave is invoicing and bookkeeping software with a free Starter plan and a low-cost Pro plan. Free plan, paid from $19/mo.Click for Scout's full analysis if you are just starting and want free books, and you don't mind recording Shopify payouts by hand.
• Choose FreshBooksFreshBooksPayments and accountingFreshBooks is invoicing and accounting software for small businesses and freelancers. Paid from $23/mo, 30-day trial.Click for Scout's full analysis if you mainly invoice wholesale or B2B buyers.

Common questions

Do I need accounting software if Shopify already shows my sales? Shopify reports cover what you sold, not your full books: bank reconciliation, bills, expenses, payroll and tax-time reports. That is the gap these tools fill.

Which accounting software has an official Shopify integration? QuickBooks Online has the Shopify Connector by QuickBooks, documented in Intuit's help center, and Xero lists a Shopify integration by Xero, free on all plans. We did not find a Shopify integration on Wave's or FreshBooks' own pages.

Which is cheapest? Wave Starter is free. Among paid plans, Wave Pro at $19/month is the lowest, followed by FreshBooks Lite at $23 and Xero Early at $27.

Are these prices billed monthly or annually? QuickBooks Online, Xero and FreshBooks publish regular monthly prices; FreshBooks also offers a yearly option with an extra 10% off. Wave Pro is $19 monthly or $190 a year.

How we put this together

We did not test these tools hands-on. Every price and feature here comes from each company's own pages, read in November 2026: the QuickBooks Online pricing page and Intuit's Shopify QuickBooks Online integration guide; Xero's US pricing page, its Shopify integration page and the Shopify app listing on the Xero App Store; Wave's pricing page; and FreshBooks' pricing page. Intro offers change often, so confirm current prices before you sign up.