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Shopify - How Shopify document synchronization with Holded works

New behavior in Shopify document synchronization with Holded

Written by Natalia López

☝🏼 Before you start

This new behavior is being rolled out to all accounts, with 15 days' advance notice. If you need it enabled on your account sooner, write to us and we'll look into it together.

Orders that already had documents in Holded before activation keep the previous behavior for their entire lifecycle. The new behavior applies to orders that come in from this point on. You can review the previous behavior in the article Shopify: sales and order synchronization – frequently asked questions.

Holded automatically syncs the orders from your Shopify store and generates the corresponding accounting documents. You don't have to create or correct anything manually.

When an already-invoiced order changes, we don't rewrite the invoice: we issue a new document that captures only what changed. The sum of all the documents for an order always matches what that order is worth in Shopify at any given moment.

The two rules that explain everything else

  1. The original invoice is never touched. A document that has already been issued and registered with the Tax Agency cannot be modified or deleted. Every correction is a new document, linked to the original.

  2. Each document captures only the difference. If you add a product, we issue the added product. If one is returned, we issue that product as a negative. We never reissue the entire order.

Credit note: in Holded you'll always see "credit note"

In Holded, every document that corrects an invoice is called a credit note, whether you're returning money or the customer is paying more. What changes is the sign of the amount:

  • Negative credit note: when money goes out to the customer. A return, a refund, or a compensation. This is what's usually called a credit note in accounting.

  • Positive credit note: when money comes in because the order increases in value. You add a product, a price goes up, or the customer switches to a more expensive size.

We use the same document type in both cases on purpose: this way, all the documents for an order stay linked to each other and to the original invoice, and you can trace the whole order from any of them. If we issued a new invoice for the increase instead, that document would be left disconnected, with no link to the rest of the order.

What does Holded issue in each case?

This table summarizes the full behavior. The following sections explain each case with an example.

What happens in Shopify

What Holded issues

When

An order comes in and is paid

A document with all the order lines, already approved

When payment is confirmed

You add a product or raise a price

A credit note with only the difference

When the change is saved

You remove units or lower a price

A negative credit note for the difference

When the change is saved

You refund part of the order

A credit note for the returned part

When the refund is settled

You refund the entire order or cancel it

A credit note that brings the order to zero

When the refund is settled

You accept a return and withhold a return fee

A credit note with the product as negative and the withheld fee as positive

When the refund is settled

The customer exchanges one product for another

A single document with the returned product and the new one

When the exchange is confirmed

You refund money without a product return

A credit note for the refunded amount

When the refund is settled

You record a return and the refund is still pending

No document while the money hasn't moved yet

When the refund is settled

You collect the outstanding balance of an order

No new document: the payment is recorded on the existing document

When payment is confirmed

You change the internal note or the order tags

Updated on the existing document, without creating anything

Immediately

You change the shipping status or address

No document

You resend the same notification or save with no real changes

No document

When is the document for a new order created?

When we receive the first notification of a new order, we create a single document (invoice, simplified invoice, or sales receipt, depending on your store's settings) with all the order lines: products, shipping, and discounts.

The document is issued already approved, dated at the time it syncs. It doesn't go through a draft stage.

Situation

What happens

The order is paid

The document is created with all the lines, already approved

The order is not paid and your store issues invoices or simplified invoices

Nothing happens until a later notification confirms payment

The order is not paid and your store issues sales receipts

It's created anyway: the sales receipt reflects the sales intent, not a confirmed income

The order is €0 and you have the option to exclude zero amounts enabled

No document

Numbering, template, warehouse, taxes, and accounting account are resolved using your store's settings, same as before. If two orders end up with the same document number, the system automatically assigns another one: documents are never duplicated.

How are payments recorded?

The document is created with the payment already attached. If you have the Shopify payment method linked to a bank account, we use that one; if not, the store's default account. If none is configured, the document is created anyway: a sale is never blocked due to missing payment configuration.

The customer pays with multiple methods

We record a separate payment for each payment method, not a combined one. This way you can reconcile each one with its bank account.

Payment method

Payment recorded

Gift card

€40.00

Card (Stripe)

€60.00

Order total

€100.00

Other payment details

• A payment authorization (money held, not yet charged) does not generate a payment. Only the actual capture does.

• If a first payment attempt fails and the second one succeeds, we only record the one that succeeded.

• If the order is paid in two installments, the document is created with the actual partial payment, and the rest is added later on the same document, without creating any new document.

• The original payment is never rewritten. If the order amount decreases after it has been invoiced, the difference is reflected in the corresponding credit note.

What happens when you edit an order that's already been invoiced?

We issue a credit note for the difference. The original invoice remains untouched.

If you add a product

Example: an order invoiced for €50.00 to which you add a €30.00 line.

Document

Amount

Original invoice

€50.00

Credit note

€30.00

Order value

€80.00

If you change a price

Example: a €100.00 invoice where you raise the price up to €120.00.

Document

Amount

Original invoice

€100.00

Credit note

€20.00

Order value

€120.00

If you make several edits in a row

Each edit generates its own document with the change relative to the previous state. Example: an order that goes from €100.00 to €80.00, then to €120.00, and finally to €90.00.

Document

Amount

Original invoice

€100.00

Credit note 1

−€20.00

Credit note 2

€40.00

Credit note 3

−€30.00

Order value

€90.00

• If you change the price and quantity of the same line at the same time, you'll see the full old line as a negative and the full new line as a positive. This is how we avoid cent-level mismatches.

• Each credit note is booked on the date the change happened in Shopify, not the date it syncs.

• If you only change the internal note or the order tags, we update those fields on the existing document. We don't create any document and we don't touch prices, taxes, or totals.

• A change in shipping status or delivery address doesn't generate any document.

• If the same notification arrives twice, a second document is not issued.

☝🏼 If you edit an order that hasn't been paid yet in stores that issue invoices or simplified invoices, the correction waits just like the first document does: we don't issue anything until payment is confirmed. The amount isn't lost, it accumulates. As soon as payment is confirmed, we issue a single document all at once with the entire difference accumulated up to that point.

Returns and refunds

Every return results in a negative document (credit note). The original invoice keeps its full sale amount; the sum of the invoice and its credit notes reflects the order's actual net amount.

The credit note amount is always the money that has actually moved. If the platform you use to manage returns withholds part of the refund, the credit note reflects the amount actually returned to the customer.

If you return part of the order

Example: a customer buys a T-shirt for €29.95 and sneakers for €89.90, with an invoice for €119.85. They return the T-shirt.

Concept

Amount

T-shirt

−€29.95

Total credit note

−€29.95

The final value of the transaction is €89.90. The credit note is applied only to the returned product.

If you return or cancel the entire order

Example: you cancel an order with a jacket for €119.00 and a cap for €24.95, and refund the €143.95.

Concept

Amount

Jacket

−€119.00

Cap

−€24.95

Total credit note

−€143.95

The order ends up at zero. If you cancel an order that hadn't been invoiced yet, we don't issue any document.

If you accept a return and withhold a return fee

We issue a single credit note. Its total is exactly the money you refund to the customer, not the product's price.

Example: a customer buys a product for €100.00. They return it and you charge them €5.00 for handling the return, so you refund them €95.00.

Concept

Amount

Product returned

−€100.00

Return fee

€5.00

Total credit note

−€95.00

The customer receives €95.00. The order doesn't end up at zero: €5.00 remains, which is exactly the return fee you charged. That amount is your income for handling the return, which is why the product is reversed in full while the document's total is only the money that went out.

It works the same way if the fee is withheld by the platform you use to manage returns: the credit note always reflects the amount actually returned to the customer.

If there are several returns on the same order

Example: on a €100.00 order, the customer first returns €30.00, and weeks later returns €20.00 more.

Document

Amount

Original invoice

€100.00

Credit note 1

−€30.00

Credit note 2

−€20.00

Order value

€50.00

If both returns are recorded at the same time, they're grouped into a single credit note of €50.00.

If the customer exchanges one product for another

We issue a single document with the returned product and the new one already netted. Never two separate documents you'd have to reconcile on your own.

Example: the customer returns a €30.00 garment and takes another size for €35.00.

Concept

Amount

Returned garment

−€30.00

New garment

€35.00

Total document

€5.00

The total is the €5.00 the customer needs to pay. If the exchange is at the same price (one size for another), the document records both lines and its total is €0.00. A return compensated with a gift card works the same way.

If you refund money without a product return

We issue a credit note for the refunded amount. The customer keeps the products and stock doesn't move.

Example: you compensate a customer with €20.00 for a delivery delay.

Concept

Amount

Adjustment

−€20.00

Total credit note

−€20.00

If the refund takes time to settle

As long as Shopify shows that the refund money is still pending transfer, we don't issue any document. We issue it as soon as the refund is no longer pending. You don't have to do anything.

When the money arrives in installments, each credit note reflects exactly the products whose refund has been settled, not the entire return.

Example: a €100.00 order with two products (A for €40.00 and B for €60.00). The customer returns both, and the refund arrives at two different times.

Moment

What Holded issues

Both returns are recorded, no refund yet

No document

The refund for product A is settled

A credit note of €40.00, only for product A

The refund for product B is settled

Another credit note of €60.00, only for product B

☝🏼 Why do we wait for the money to move?

When you refund or cancel an order, Shopify does two things at different times. First it records the return, which is what you see on the order instantly. Then it moves the money through the payment gateway, which takes longer.

While that second step is still pending, the refund isn't yet a firm fact: the gateway could reject it. A credit note is, because it's registered with the Tax Agency and can't be rewritten afterward.

That's why we wait until no refund movement is still pending before issuing the document.

Taxes

The VAT rate for each line is resolved using your account's settings, following this order:

Situation

Tax applied

Shopify reports the tax for the line

The country tax rule that applies, based on the shipping address (or the billing one if there's no shipping)

There are no country rules or the order has no address (POS sale)

Your account's default country

The line arrives with no tax information

The contact's default tax and, if it has none, the store's

The line arrives with an explicit 0%

The 0% is respected as a deliberate exemption

Your store's prices include tax

We separate base and tax before creating the line

The reconciliation adjustment line

When closing each document, we check that the sum of the lines matches exactly the official amount of the order in Shopify. If there's a rounding difference of a few cents, we add a visible adjustment line so the document closes at your store's exact amount.

This is a rounding adjustment, not a real charge or discount. You'll see a line like this, for example, on orders that mix products with different VAT rates.

When don't we issue any document?

Situation

Reason

The order isn't paid and your store issues invoices or simplified invoices

We wait for payment confirmation; the amount accumulates and isn't lost

The refund for a return is still pending transfer

We wait for the money to actually move

The order is €0 and you have zero-amount exclusion enabled

Your store's settings

The order carries an excluded tag

Your store's settings

The shipping status or delivery address changes

It doesn't affect the document's content

The notification arrives again, or you save the order with no real changes

There's no difference to reflect

You cancel an order that hadn't been invoiced yet

There's nothing to correct

You don't need to configure anything

• The whole process is automatic: there are no documents to create and no credit notes to issue by hand.

• Every sale, edit, return, or refund recorded in Shopify is reflected in your documents.

• Invoices that have already been issued are never modified. Every correction is a new document linked to the original.

• The sum of all the documents for an order always matches what that order is worth in Shopify.

A note on scope

This behavior is available today for Shopify and is enabled per account. If you have several Shopify stores under the same account, it's enabled for all of them at once.

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