Skip to main content

Installation manual for the Shopify Yuki integration

Updated today

Connect Shopify with Yuki and automatically process orders in your accounting. Shopify orders are directly visible in Yuki. Save time on your administration.


Table of contents


1. Connect to Shopify

You install a Combidesk connection directly from the Shopify App Store. Log in to the Shopify App Store and search for the app you want to install. Click Install on the app page.

Before the installation is completed, Shopify displays an overview of the data and parts of your store that the app is requesting access to (Shopify Help Center).
Read through this and then click Install to confirm.

After clicking Add app, you authorize the connection to read and/or write data from your webshop. Once that is done, the connection with Shopify is established and you will be automatically redirected to the configuration steps where you can set up the connection further. After completing all the steps, you approve the monthly license fee.

Your installed apps can always be found afterwards via Settings → Apps in your Shopify admin environment (Shopify Help Center).


2. Connect to Yuki

In Yuki, go to Settings > Integrations > Web Services. Click the black plus icon in the top left and create a new web service. Select the correct administration and grant all permissions. Copy the API key that appears. Finally, click Save. Then enter the API key for this Yuki web service in Combidesk.

I can't find the API key

If you don't see a "Web Services" option in Yuki, you most likely don't have sufficient permissions. To manage web services, you need at least the "Backoffice" or "Management" role.


3. Configuration of the integration

For the integration to work properly, it must be configured correctly. In the paragraph below, we'll go through all the steps of the integration in sequence. Before starting the installation, we recommend that you first carefully read through these steps.


Configure these Shopify steps:

  • Based on which status should orders be synced to Yuki?
    Please indicate below for which order status(es) the app should synchronize the order. Please note: once an order has been synchronized to Yuki, any subsequent changes in Shopify will no longer be updated in Yuki.

    Are you using a Payment Service Provider (PSP)? Please note that the order must be in Yuki before the payment, otherwise the payment cannot be matched with the outstanding item.

  • Export existing orders
    Do you want to export existing orders from Shopify

  • Fullfillment date
    Should the fulfillment date be used as the order date?

  • Do you want to add prefixes and suffixes to order numbers?
    If you choose 'No' order numbers will be transferred as-is. If you choose 'Yes' the prefix and suffix that you have configured in Shopify (at Settings > Store details > Order ID format) is added to the order number. Note: existing orders won't be adjusted. Read this article (Dutch) for more information on prefixes and suffixes in Shopify.

    Choose 'Yes' when you connect multiple Shopify stores to the same bookkeeping administration.

  • Add discount order lines
    Do you want the discount on a separate order line?

  • Export existing refunds
    Do you also want to export refunds from Shopify. Note: Cancelled orders are not considered refunds.

  • Sync Shopify Payments transactions?
    Are you using Shopify Payments as your payment service provider (PSP)? If so, you can indicate here whether you want received payments to be automatically processed in your accounting.

    Choose "Yes" if you want the payouts from Shopify Payments to be automatically matched to the corresponding open entries in your accounting after settlement. Additionally, the associated transaction fees will be posted automatically. This automates the reconciliation process within your accounting.

    Choose "No" if you are not using Shopify Payments, or if you prefer to track the payments manually in your accounting software.

  • Export existing Shopify Payments transactions
    Do you want to export existing Shopify Payments transactions?


Configure these Yuki steps:

  • Select administration
    Select the administration to connect to

  • Map the vat types
    Map the Shopify vat categories on the vat types of Yuki to create sales invoices

  • Sending costs
    Enter the description of the article to book the sending costs on

  • Other costs
    Enter the description of the article to book the other costs on

  • Book revenue
    How would you like the revenue to be booked?

  • Ledger account mapping per country
    Map the countries of Shopify to the corresponding ledger accounts from Yuki

  • Ledger account mapping
    Map the vat categories of Shopify to the corresponding ledger accounts from Yuki

  • Default ledger account
    Select the default ledger account for products that are created in Yuki

  • Default debtor
    If you want to book your orders on a default debtor, enter the code of that default debtor here

  • Debtor for Point of Sale (POS) orders
    Do you use Point of Sale (POS) in Shopify? Then you can also automatically post POS orders in Yuki. Enter the Relation Code of the debtor in Yuki to which these orders should be posted. You can find the Relation Code in Yuki via: Relations → [debtor name] → Extra tab → Relation Code. No POS debtor in Yuki yet? Click "Create debtor" to add one automatically.

  • Payment method B2B
    Select a default payment method for the invoices to commercial customers.

  • Payment method B2C
    Select a default payment method for the invoices to private customers.

  • How do you want to handle VAT for orders to individuals in other EU countries (One-Stop Shop, OSS)?
    Do you ship to individuals in other EU countries? Then you can pick one of the VAT arrangements below. If you want to keep using the rules of before July 1, 2021, select "Charge VAT based on the webshop's country", then the regular VAT of your country will be charged.

    For more information, please see this Yuki article (Dutch).

  • Service level
    Pick a Service level matching your needs. You can always change the it at a later time, and the price will be adjusted accordingly.

  • IBAN
    Enter the IBAN of the bank account to book the online payments on


4. The Combidesk customer dashboard

How does the dashboard work?

If you've created a new Combidesk account or installed a integration, you'll receive an email with access to your Combidesk account. When you log in to combidesk.com, you'll arrive at the dashboard. This is where your integration is located. From here, you can easily adjust your integration and account settings, view the integration logs (history), and access support.

What can you view via your Combidesk account?

From your Combidesk dashboard you also have access to your account settings, connected accounts, billing and support.


5. What can you expect from Combidesk?

We understand you're busy or perhaps have little software experience. That's why our specialized team is always ready to help. Take advantage of our installation packages to save yourself even more time.

Installation appointment

If you're short on time or would like us to handle the entire installation, take advantage of our remote implementation support. We'll take care of everything for you right away and deliver a fully functional connection. For most connections, installation support costs a fixed fee of €150, while others cost €300. If you decide not to continue with the connection after the trial period, there's no charge. Schedule an installation appointment below and schedule it right away.

Explanation of service level (SLA) subscriptions (Basic, Pro, Premium)

To help you use our integration effectively, we offer three service levels: basic, pro, and premium. You can always change the service level in your integration. The price will be adjusted for the next billing period.


6. FAQ (Frequently Asked Questions)

How often are the data synchronized?

This integration synchronizes automatically every 60 minutes by default. You don't need to do anything for this. If a synchronization fails, the integration will try again on the next run. If the issues persist, you will be notified by email.

Can the PDF of the order be included when sending it to Yuki?

No, unfortunately, technically the PDF cannot be read and therefore cannot be included when sending it to Yuki.

Can I connect multiple Shopify webshops?

Certainly. For this, you need to install the integration separately for each webshop.

Should I synchronize products?

The integration synchronizes the Shopify products to Yuki so that they can be used in the sales invoice. This process happens automatically.

Is inventory synchronized?

No, the integration does not synchronize items to Yuki. Therefore, it is recommended to manage your inventory in Shopify.

Are credit orders also added, and how does that work exactly?

Yes, the integration also synchronizes refunds. When you refund (credit) a Shopify order, a sales invoice with a negative amount will be created in Yuki for that order. PLEASE NOTE: Cancelled orders are not forwarded, so do not cancel an order if it still needs to be synchronized as a credit order.

Can you help with the installation of this integration?

Absolutely 😀! If you don't have the time or find the setup too complicated, no problem! We can handle the installation of this integration for you. There will be a one-time installation fee for this service. If you later decide not to use the integration, we'll refund the installation fee to you.

How do I get the correct VAT on a Yuki invoice?

Make sure that you have activated the VAT rates used in both Shopify and Yuki. In the integration, you can then link these VAT rates together.

Did this answer your question?