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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.

Updated:

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 Malta

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

VAT
Rates 18 %, 12 %, 7 % and 5 %. Malta has no zero rate in law. Exports, EU supplies, food and medicines are exempt with credit, which lets you reclaim input VAT. Exempt without credit does not.
Article 11 small undertakings
With up to €35,000 of domestic turnover a year you can be exempt under Article 11. The status ends on the day the limit is passed, and you still register with the VAT department. Saldiqo adds the exemption note and leaves VAT off.
Tax invoice or fiscal receipt
A tax invoice is issued only when the customer gives you a VAT number. Otherwise a fiscal receipt from an approved system is required. Saldiqo writes invoices. It is not a fiscal receipt system, and a Saldiqo PDF does not replace a fiscal receipt.
Invoice timing
Issue the invoice by the 15th of the following month, or when payment arrives if that comes first. Simplified invoices are allowed up to €100.
E-invoicing
There is no mandate. Public bodies accept e-invoices through Peppol (EN 16931). The tax authority plans e-invoicing and real-time reporting but has set no dates, and EU rules apply from 1 July 2030.
VAT returns
Returns are due by the 15th day of the second month after the period, with 7 extra days when you file and pay electronically. Article 11 businesses file a yearly declaration by 15 February. Saldiqo does not file returns.
Record keeping
VAT records for 6 years, income tax records for 9 years and company records for 10 years. Plan for 10 years.
Late payment
Interest on late business payments is 10.40 %, plus €40 compensation between businesses.
Languages
Use Saldiqo in English or Maltese and send invoices in either language.

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 Malta have to charge VAT?

If you are registered under Article 10, yes. Small undertakings under Article 11 with domestic turnover of up to €35,000 a year are exempt from charging VAT, but the status ends on the day the limit is passed.

Do Shopify stores in Malta need a fiscal receipt?

Sales to consumers need a fiscal receipt from an approved fiscal receipt system, and Article 11 businesses use one for all sales. Saldiqo is not such a system. It covers tax invoices to customers who give you their VAT number.

How long should Shopify stores keep invoices?

VAT records for 6 years, income tax records for 9 years and company records for 10 years, so plan for 10 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.