How to Connect Shopify, Stripe or HitPay to Xero (Singapore)

Why your bank deposits never match your sales

A S$100 sale doesn't arrive in your bank as S$100. Between the sale and the deposit, three things happen:

• Fees are deducted: the payment provider's card or PayNow fee, and on Shopify any app or third-party transaction fees.
• Payments are batched: one payout can cover dozens of orders over several days.
• Refunds and disputes are netted off against new sales.

If you record each payout as "sales" in Xero, your revenue is understated, fees are invisible, and GST can be wrong. If you record each order and then also the payout, you count sales twice. The integrations below, combined with a clearing account, record the gross sale, the fee and the payout separately so everything lines up.

The three integrations at a glance

Xero itself costs S$39, S$70 or S$95 a month for the Starter, Standard and Premium plans, in SGD including GST, per Xero's Singapore pricing page as of October 2026.

Shopify to Xero

Xero now offers its own Shopify integration. According to its Xero App Store listing:

• it syncs sales, payouts, fees and taxes from Shopify into Xero;
• you choose a daily summary (one entry per day, best for high-volume stores) or per-sale transactions (customer and line-item detail);
• it reconciles payouts from Shopify Payments and other providers against your bank feed, handling fees, refunds and taxes;
• it includes Shopify POS sales alongside the online store;
• you map Shopify taxes to Xero tax rates;
• it can sync up to 90 days of historical data when you first connect.

If you take PayNow on Shopify through HitPay, those payouts come from HitPay rather than Shopify Payments, so map them to their own clearing account.

Stripe and HitPay to Xero

Stripe

The Stripe app in the Xero App Store lets customers pay Xero invoices by card through Stripe, and brings Stripe transaction data into Xero so you can reconcile each payment. The Xero listing notes that automatic payment on repeat invoices is only available on approved repeat invoice templates. Payouts follow your Stripe schedule; Stripe says the first payout typically takes 7 to 14 days (Stripe payouts).

HitPay

HitPay's Xero app adds PayNow QR to Xero online invoices, plus cards, Apple Pay, Google Pay, WeChat Pay and Alipay, and syncs payment data for reconciliation. For local B2B clients who prefer PayNow, this is often the simplest way to get invoices paid faster.

Choosing between them? Our guide to HitPay vs Stripe in Singapore compares fees, payouts and features.

The clearing account method, step by step

A clearing account is a holding account in Xero that sits between your sales and your bank. Sales go in, fees and payouts come out, and when everything is recorded correctly its balance returns to zero (or to the money still waiting to be paid out).

1. In Xero, create a bank-type or current-asset account for each provider, for example "Shopify Payments clearing", "Stripe clearing", "HitPay clearing".
2. Point the integration's sales and fees at that clearing account, and map fees to an expense account such as "Payment processing fees".
3. When a payout lands in your real bank account, reconcile it in the bank feed as a transfer from the clearing account.
4. Check the clearing account balance each month. It should equal payouts in transit; a growing balance means something isn't being recorded.
5. Record refunds and disputes through the integration, not by hand, so they also flow through the clearing account.

Ask your bookkeeper or accountant to agree the account set-up before you connect anything. Changing it after months of synced data is painful.

GST and other settings to check

• GST-registered? Map Shopify taxes to the right Xero tax rates, and check whether your store prices include GST.
• Payment fees: decide with your accountant how fees from Stripe, HitPay and Shopify are treated for GST in your books.
• Multi-currency: if you sell overseas, check how foreign-currency sales and conversion fees come through.
• Invoices: if you are GST-registered, check where you stand with InvoiceNow. Our InvoiceNow (Peppol) guide explains the timeline and setup.
• Access: connect integrations with an admin account that has MFA on, and remove access for anyone who no longer needs it.

IT Sorted sets up the connections; we don't give tax advice or do bookkeeping. Your accountant should confirm the tax treatment.

Do it yourself or get help?

Connecting a single Shopify store or Stripe account to Xero is a reasonable do-it-yourself job if you set up the clearing account first and test with a few days of data.

The Xero / QuickBooks Integration (S$390) connects Xero or QuickBooks to Stripe, HitPay or Shopify, connects your bank feed, brands your invoice templates, sets up automatic payment reminders and gives your bookkeeper a short guide. If you don't have a payment account yet, Online Payment Setup (S$290) gets Stripe or HitPay running first.