Your accounting runs itself.
Your numbers stay clean.

Use a dedicated reconciliation tool like A2X or Synder, not manual deposit matching. A2X breaks every Shopify payout into gross sales, refunds, discounts, gift cards, shipping, taxes, and processor fees, then posts each to the right account in QuickBooks or Xero. That's the only way to get clean gross margin reporting at scale.

A2X is accounting automation built specifically for Shopify, Amazon, Etsy, and Walmart sellers. It takes the raw payout data and turns it into a single journal entry per payout that's fully broken out by line item type. If you're doing more than about $30K/month on a single ecommerce platform, yes, you need A2X or equivalent — manual reconciliation stops scaling fast.

You need two things: accurate sales data broken out by channel and SKU (which A2X or Syft gives you), and a chart of accounts that separates COGS by channel. Then reporting tools like Syft or a custom dashboard can show you gross margin by Shopify vs Amazon vs wholesale. On the Growth plan we build this reporting so you can see which channel is actually paying rent.

Amazon is harder than Shopify because settlements include FBA fees, storage, advertising, refunds, reserves, and returns all in one deposit. A2X handles Amazon specifically and breaks each settlement into the right categories automatically. Without a tool like A2X, Amazon reconciliation is the single biggest reason ecommerce books end up behind.

QuickBooks Online is the practical default — it integrates with every ecommerce tool and most CPAs know it. Xero is a strong alternative, especially for Canadian businesses or multi-entity setups. Skip the ecommerce-native tools (A2X, Syft, Dext) for the books themselves; they integrate into QBO or Xero, they don't replace them.