You’ve done your stocktake, your inventory numbers are sorted, and now your accountant is asking for your sales data. If your Shopify store isn’t connected to Xero, this is the part where things can get a bit fiddly. Here’s what you need, how to get it, and why connecting the two is worth doing if you haven’t already.
What your accountant actually needs
Every accountant is a little different, but at end of financial year for a Shopify store, they’ll generally want to see:
Your total sales for the year, broken down by gross sales, discounts, refunds, and net sales. Shipping revenue if you charge for it. Your payment processing fees, since these are a business expense. Any Shopify subscription fees paid during the year. And your GST collected, which needs to reconcile with what you’ve filed or will file with IRD.
The good news is Shopify has all of this. The question is how you get it out in a format that’s actually useful.
Exporting your sales reports
Head to Analytics > Reports in your Shopify admin. The reports you’ll want to pull for year end are:
Sales over time, set to the full financial year from 1 April 2025 to 31 March 2026. Export this to CSV. This gives your accountant a clear picture of revenue over the year.
Finances summary, which breaks down gross sales, discounts, returns, shipping, taxes, and net sales all in one place. This is often the most useful single report for an accountant.
Payments, which shows what came through each payment gateway and what fees were charged. If you’re on Shopify Payments, your processing fees sit here.
Export each of these to CSV and send them through. If your accountant uses Xero, they can import and work with these directly, but it’s still a manual process.
A note on GST
If you’re GST registered in New Zealand, your Shopify store should be set up to collect 15% GST on applicable sales. Shopify’s taxes report shows what GST was collected over any date range you set. Pull this for the full financial year and check it against what you’ve filed in your GST returns. If there are discrepancies, flag them with your accountant before year end rather than after.
Worth knowing that GST on Shopify’s own fees, like your monthly subscription and transaction fees, is also something your accountant will want to account for. Shopify charges GST on these for NZ businesses.
Reconciling your sales against bank deposits
This is where a lot of store owners get unstuck. The amount Shopify deposits into your bank account is not the same as your total sales. Shopify batches transactions, deducts processing fees, and pays out on a rolling schedule. So a single bank deposit might represent several days of orders minus fees and refunds.
If you’re on Shopify Payments, your payout report in Finances > Payouts shows exactly what orders are included in each deposit, what fees were deducted, and what the net amount was. That makes reconciliation pretty straightforward.
Worth knowing that while Shopify’s payments report shows transactions across all your payment methods including Afterpay and any other buy now pay later providers, each one deposits into your bank account separately. So you’ll have one deposit from Shopify Payments, a separate one from Afterpay, and so on. The payments report gives you the totals for each gateway, and you reconcile those against the corresponding deposits in your bank feed. If you ever need a detailed breakdown of an Afterpay settlement, you can download that from your Afterpay merchant portal.
Connecting Shopify to Xero: the easier way
If you’re doing this manually every month or scrambling at year end, it’s worth knowing there’s a better way. Connecting Shopify to Xero means your sales data flows across automatically every day, payouts reconcile against your bank feed, and your accountant has everything they need without you having to export a single spreadsheet.
There are three main options for connecting the two.
Xero’s native Shopify integration is available directly from the Xero App Store at $13 USD per month for NZ users. It creates a daily summary invoice per payment gateway and handles GST grouping for NZ. It’s the simplest option to set up, but it has mixed reviews and doesn’t cover inventory, multi-currency, split sales, or individual order detail. Worth knowing before you commit.
Amaka is a well-regarded third-party integration that syncs sales, fees, refunds, COGS, gift cards, taxes, and payment types to Xero automatically each day. It handles bank reconciliation by matching transactions to your Shopify payouts, and you can choose between a daily summary or per-order invoices depending on what your accountant prefers. There’s a free plan for up to 60 transactions a month, with paid plans from there. Worth noting it also works with MYOB if you’re not on Xero. You can find out more at amaka.com.
A2X is the option most ecommerce accountants recommend for higher volume or more complex stores. It creates settlement journals that match exactly to your Shopify payouts in your bank feed, handles COGS, multi-currency, and scales well as your store grows. It also supports multiple sales channels including Amazon, eBay, Etsy, and Walmart, so if you’re selling across more than one platform it can bring everything into Xero in one place. More detail at a2xaccounting.com.
Either way, once it’s set up you’re not thinking about it. Your books stay up to date, your accountant has what they need, and year end becomes a much smaller event.
If you’re not sure which option is right for your store, have a chat with your accountant before you set anything up. They’ll have a preference and it makes sense to set it up in a way that works for how they manage your books.
Want help getting your store connected to Xero?
It’s one of those things that’s a bit fiddly to set up but makes everything easier once it’s done. If you’d like a hand, we’re happy to help.
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