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Accounting and invoicing for Shopify stores

Orders by the minute, discount codes, returns, payouts from payment providers and ad costs: a Shopify store has many data sources and little time for paperwork. Saldiqo fetches orders from Shopify, writes invoice and delivery note, records payouts and shows what is left after fees and advertising.

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What comes up for Shopify stores

Many orders

Every order needs an invoice, a delivery note and a payment received.

Payouts and fees

Payment providers pay out in bundles and deduct fees.

Ad costs

Ads are the biggest expense of many stores. Invoices come from several platforms.

How Saldiqo helps

  • Connect ShopifyEnter the access details, fetch orders.
  • Match payoutsUpload the bank statement.
  • Record ad costsPlatform invoices as expenses.
  • ReturnsCredit note with a link.

Typical invoice lines

Examples that often appear on invoices in this industry. You set the prices yourself.

  • Items as per order
  • Shipping as per order
  • Discount code, deducted
  • Credit note: return
  • Payment provider fee as per statement
  • Ad costs as per receipt

Tax and invoicing in the UK

What applies to invoices in the UK, in short. As of October 2026.

VAT
Standard rate 20 %, reduced rate 5 % and zero rate 0 %. Saldiqo calculates each invoice line with the rate you pick.
VAT registration
You must register once your taxable turnover passes £90,000 over any 12 months, or you expect to pass it within the next 30 days. You can deregister below £88,000. Until you are registered, your invoices show no VAT, and Saldiqo adds up your 12-month turnover for you.
What goes on an invoice
If you are VAT registered: your VAT number, the tax point, unit prices and the VAT total in pounds. A limited company shows its registered name on every invoice, and its company number, registered office and part of the UK on letters, order forms and the website.
E-invoicing
There is no mandate today. From April 2029 e-invoicing is planned for all B2B and B2G sales that carry VAT, through Peppol. The exact date and standard are not yet in law, and the government’s roadmap follows with the Budget on 28 October 2026.
VAT returns
VAT returns go to HMRC through Making Tax Digital, usually quarterly, due one month and seven days after the period. Saldiqo shows sales and VAT per rate and exports CSV. It does not submit to HMRC, and for Making Tax Digital you need software recognised by HMRC.
Record keeping
Keep VAT records for 6 years.
Late payment
Statutory interest on late business payments is the Bank Rate (3.75 % in the second half of 2026) plus 8 points, so 11.75 %. On top comes fixed compensation of £40, £70 or £100, depending on the amount owed (under £1,000, from £1,000, from £10,000). Consumers have no statutory interest.
Getting paid
Your sort code and account number are on every invoice. Customers pay by Faster Payments or Bacs, and banks check the account name with Confirmation of Payee. There is no QR standard in the UK.

Frequently asked questions

How do I connect Shopify?

You enter your shop address and the access token of your own app. Saldiqo reads orders and reports shipping back if you like.

How do I treat payouts?

You upload the bank statement, match receipts to orders and record fees as an expense.

Do Shopify stores in the UK have to charge VAT?

Only once they are VAT registered. Registration is required when taxable turnover passes £90,000 over any 12 months, or is expected to within the next 30 days. Below that you may register voluntarily. If you are not registered, you must not show VAT on your invoices.

Do Shopify stores in the UK need e-invoicing?

Not today. A mandate for B2B and B2G sales with VAT is planned from April 2029, and the details were still open as of October 2026. You can keep sending PDF invoices for now.

How long should Shopify stores keep invoices?

Keep VAT records for 6 years. You can store receipts digitally in Saldiqo. The legal duty to keep records stays with you.

Try Saldiqo for free

Write invoices, match payments, collect receipts and send reminders: free and without a trial period.

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As of October 2026. General information, not legal or tax advice, without guarantee. For your case ask your tax adviser.