October 31 is the deadline for the VAT return over the third quarter. For webshop owners who use Shopify and track their administration in Moneybird, there are a few specific things to check before submitting the return. Use this checklist to make sure everything is correct and you don’t miss any VAT or overpay.
1. Check all Shopify orders from July through September
Start with the basics: are all Shopify orders from July 1 through September 30 present in Moneybird as invoices? Open Moneybird, filter on sales invoices for the period July through September and compare the total with your Shopify order overview for the same period.
A discrepancy indicates missing orders. This can happen due to a temporary interruption of the connection, a platform update in Shopify, or orders that weren’t synchronized for another reason. With Schakel you can run a manual re-sync to fill any gaps. Also check whether your test orders are correctly excluded or processed as zero amounts, as these would otherwise distort your VAT base.
2. Process all returns as credit notes
Every refund or return that took place in the third quarter must be recorded in Moneybird as a credit note. Go through your Shopify returns from July through September and check whether each case has a corresponding credit note. Missing credit notes inflate your revenue and cause you to pay too much VAT.
This is one of the most common mistakes during the quarterly return: the return is in Shopify but not in the accounting. An automated connection solves this because credit notes are created directly as soon as a refund is processed. More about how this works in practice in our article on credit notes and returns in Shopify.
3. Check VAT rates per transaction
Not all products fall under the same VAT rate. In the Netherlands the high rate of 21% applies to most goods, but for certain categories such as specific foods, medicines and books the rate is 9%. Check whether all invoices in Moneybird contain the correct rate, especially if you sell products in both categories.
Shopify automatically applies VAT rates based on the product category you’ve set, but errors in product configuration lead to incorrect VAT codes in Moneybird. Review products with unusual or variable categorization extra carefully. More about correctly setting VAT rates in the Shopify-Moneybird connection in our article on VAT in Moneybird and Shopify.
4. Process EU sales via the OSS scheme
Do you sell to consumers in other EU countries? Then you must account for that revenue through the OSS return, not through your regular Dutch VAT return. Check in Moneybird whether all EU transactions are created with the correct OSS coding and are separated from your Dutch revenue.
The threshold for OSS is 10,000 euros per year in cross-border EU B2C revenue. If you’ve already passed that threshold earlier this year, you automatically fall under OSS for the remainder of the year. Check your cumulative EU revenue in Moneybird to determine whether this applies to you. More information in our article on OSS and EU sales via Shopify.
5. Reconcile your bank account with Moneybird
Before submitting the return, it’s wise to reconcile your bank account in Moneybird with your actual bank statement. Import all bank statements from July through September if you haven’t done so yet and link outstanding lines to the corresponding invoices.
Note: Shopify Payments pays out your gross revenue minus transaction fees. The amount on your bank statement is therefore lower than the sum of your invoices. In Moneybird you book the transaction fees as a separate cost item, so the balance works out. How to process this correctly is described in our article on Shopify payouts and transaction fees in Moneybird.
6. Generate the VAT report in Moneybird
Go to Reports in Moneybird and generate the VAT report for the period July 1 through September 30, 2026. This report gives you an overview of all VAT payable and deductible, broken down by rate. Check whether the amounts match what you expect based on your revenue and purchases.
Discrepancies in the report are always a signal to investigate further, not to ignore. An amount that seems too high or too low almost always points to a booking that’s incorrect. Resolve this before submitting the return, because submitting a corrected return later costs more time and attention than a correct return the first time.
7. Submit the return via the Tax Authority
Once your Moneybird administration is correct, submit the VAT return via Mijn Belastingdienst Zakelijk. The deadline is October 31, 2026. Submit on time, even if you expect a refund: a late return always leads to a fine, regardless of whether you owe money or are getting money back.
If you have an accountant, make sure to deliver the data from Moneybird well before October 31 to allow time for review and processing. An exportable VAT report from Moneybird makes this straightforward.
Automate your quarterly routine
Most steps in this checklist become much easier when you keep Shopify and Moneybird automatically synchronized. Schakel ensures that every order immediately appears as an invoice in Moneybird and every refund is created as a credit note. That way you start the quarterly review with an administration that’s already largely up to date, rather than having to work through a backlog first.
For a complete overview of all tasks at the quarterly closing, read our article on the quarterly closing checklist for Shopify in Moneybird.
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