--- title: "Accounting software setup & migration for e-commerce brands & amazon sellers" description: "Accounting software setup & migration for e-commerce brands & amazon sellers: quickBooks, Xero, Zoho Books and Sage setup, plus migration from Bench." url: https://ledgerbpo.com/industries/ecommerce/accounting-software-setup/ updated: 2026-09-11 publisher: LedgerBPO (SS Support Network LLC) language: en-US --- # Accounting software setup & migration for e-commerce brands & amazon sellers QuickBooks setup for e-commerce brands & amazon sellers starts with a chart of accounts that separates gross sales from refunds, marketplace fees, processing fees, advertising and fulfillment by channel, plus inventory, in-transit stock, supplier prepayments, deferred revenue and sales tax collected by facilitator versus by you. Your accountant designs the accounts, connects A2X or Link My Books to Amazon, Shopify and other channels, maps every fee type, sets up PayPal, Stripe and instalment gateways as accounts, links Dext or Bill.com for supplier bills and Gusto for payroll, and loads opening balances from reconciled figures. - Since 2020 - US · UK · CA · AU - Named accountant plus backup - Your software, no lock-in [Get a custom quote](https://ledgerbpo.com/get-a-quote/) [Book a 20-minute call](https://ledgerbpo.com/book-a-call/) Updated September 2026 ## How it runs for e-commerce brands and Amazon sellers Xero setups follow the same design with tracking categories per channel. ## What is accounting software setup and migration? Accounting software setup is the configuration of a new ledger: chart of accounts, tax codes, bank feeds, items, users and apps. Migration is moving existing books from another platform or spreadsheet into that ledger so history, open items and balances carry across. Both end with a file that agrees to the old records and is ready for live posting. ## What we handle for e-commerce brands and Amazon sellers - Chart of accounts with sales, refunds, fees and advertising by channel - Inventory, in-transit, prepayment and deferred revenue accounts created - A2X or Link My Books connected with every fee type mapped and tested - PayPal, Stripe and instalment gateways set up as reconcilable accounts - Opening inventory and balances loaded from reconciled reports ## The KPI that matters here Setup complete with a tested settlement posting and reconciled opening balances before the first live month. ## E-commerce compliance notes ### Marketplace facilitator laws Every US state with a sales tax now requires marketplaces such as Amazon, Walmart, eBay and Etsy to collect and remit sales tax on third-party sales. The marketplace's collections appear in your settlement reports and must be recorded as tax collected and remitted by the facilitator, not as your liability. Some states still require registered sellers to file returns that report marketplace sales as exempt. ### Sales-tax nexus on direct sales Direct sales through Shopify, your own site or wholesale count toward each state's economic nexus threshold, commonly $100,000 in sales or 200 transactions in the current or prior year, and inventory stored in FBA warehouses can create physical nexus. We track sales by state monthly, flag thresholds approaching and prepare the workings for TaxJar, Avalara or your filing provider. Registration and filing decisions rest with you and your tax adviser. ### VAT, GST and cross-border selling Selling into the UK requires VAT registration once taxable turnover passes £90,000, or from the first sale for many overseas sellers, and EU distance sales can be reported through the One Stop Shop. Canadian GST/HST and Australian GST apply to imported low-value goods and to registered sellers. We prepare VAT and GST workings for your accountant or registered agent to file; we do not submit returns. ### Inventory valuation and 1099-K reporting Inventory must be valued consistently, including freight, duties and prep, so COGS and taxable income are right. Payment processors and marketplaces issue Form 1099-K for gross payments, which is reconciled to recorded sales so the figures your CPA reports agree with what the IRS receives. Tax preparation is support only; your firm reviews and signs. ## E-commerce software we work in - [Shopify](https://ledgerbpo.com/software/shopify/) - [Amazon Seller Central](https://ledgerbpo.com/software/amazon-seller-central/) - [A2X](https://ledgerbpo.com/software/a2x/) - [Link My Books](https://ledgerbpo.com/software/link-my-books/) - [QuickBooks Online](https://ledgerbpo.com/software/quickbooks-online/) - [Xero](https://ledgerbpo.com/software/xero/) - [Stripe](https://ledgerbpo.com/software/stripe/) - [PayPal](https://ledgerbpo.com/software/paypal/) - [TaxJar](https://ledgerbpo.com/software/taxjar/) - [Avalara](https://ledgerbpo.com/software/avalara/) - [Bill.com](https://ledgerbpo.com/software/bill-com/) - [Gusto](https://ledgerbpo.com/software/gusto/) - [All 50 platforms](https://ledgerbpo.com/software/) ## More for e-commerce brands and Amazon sellers Other services for e-commerce - [Bookkeeping](https://ledgerbpo.com/industries/ecommerce/bookkeeping/) - [Invoicing and billing](https://ledgerbpo.com/industries/ecommerce/invoicing-and-billing/) - [Accounts receivable](https://ledgerbpo.com/industries/ecommerce/accounts-receivable/) - [Accounts payable](https://ledgerbpo.com/industries/ecommerce/accounts-payable/) - [Bank reconciliation](https://ledgerbpo.com/industries/ecommerce/bank-reconciliation/) - [Month-end close](https://ledgerbpo.com/industries/ecommerce/month-end-close/) - [All e-commerce services](https://ledgerbpo.com/industries/ecommerce/) Software setup and migration in other industries - [Marketing agencies & consultancies](https://ledgerbpo.com/industries/agencies/accounting-software-setup/) - [Auto repair shops & dealerships](https://ledgerbpo.com/industries/auto/accounting-software-setup/) - [Behavioral health practices](https://ledgerbpo.com/industries/behavioral-health/accounting-software-setup/) - [Daycares, schools & education](https://ledgerbpo.com/industries/childcare-education/accounting-software-setup/) - [The full software setup and migration page](https://ledgerbpo.com/services/accounting-software-setup/) ## Frequently asked questions ### Should Shopify orders post individually or as summaries? Summaries by payout are usually better. Posting thousands of individual orders slows the file, clutters the customer list and still needs a payout reconciliation. A2X or Link My Books posts one journal per payout with sales, refunds, fees and tax mapped, and the accountant reconciles it to the deposit. Order-level detail stays in Shopify where it belongs. ### How do you set up sales tax accounts for marketplace and direct sales? Tax collected and remitted by marketplaces is mapped to a facilitator-collected account that nets to zero, while tax you collect on direct sales is mapped to a liability by state or jurisdiction. TaxJar or Avalara is connected for the direct channel. This keeps your liability accurate and the marketplace figures available for returns that require them. ### Can you migrate an e-commerce brand from Xero to QuickBooks Online or the reverse? Yes, the migration moves lists, balances and history, and the accountant rebuilds the channel structure, fee mappings, inventory accounts and gateway accounts that do not transfer cleanly. A2X or Link My Books is reconnected to the new file. Reports for the prior period are compared before and after cut-over so nothing is lost. Next step ## Books closed. Invoices paid. Every month. Tell us what is going on with your books or billing. You will hear from a named person within 1 business day, with a custom quote and a plan for the first close. - Reply from a named person within 1 business day - No setup fee, month-to-month - Your software, your data, no lock-in Start with a custom quote [Get a custom quote](https://ledgerbpo.com/get-a-quote/) [Book a 20-minute call](https://ledgerbpo.com/book-a-call/) Or call [+1-657-777-0006](tel:+16577770006) during US, UK or Australian business hours. --- Source: https://ledgerbpo.com/industries/ecommerce/accounting-software-setup/ · Contact: https://ledgerbpo.com/contact/ · Full site map for agents: https://ledgerbpo.com/llms.txt