Payments, integrations and omnichannel on Shopify: the complete overview
Payments, integrations and omnichannel on Shopify are three disciplines that, in practice, depend deeply on one another. A customer expects to pay with their preferred method, whether they are shopping on your webshop, in the physical store or through a marketplace. Behind the scenes, that requires orders, inventory and payments to flow freely between Shopify and the other systems your business already uses.
At Mercive we see many brands that have the webshop itself under control but lose the overview once payment flows, ERP, inventory and physical sales channels need to work together. This article is the hub of our topic collection on exactly that. We give you a structured overview and point along the way to the in-depth articles where you can dig into each area.
Payments: Shopify Payments and local payment methods
Shopify Payments is Shopify's own built-in payment solution, which lets you accept card payments directly in checkout without setting up a third-party gateway. It makes setup simpler, because transactions and payouts are managed in the same place as your orders. In the Danish market, many brands combine it with gateways like Quickpay to cover local methods such as MobilePay, where the customer is sent to a payment window and completes the payment there.
A frequent question is how many percent Shopify takes. There are two types of cost to keep separate: the transaction fee to the card acquirer that processes the payment, and a possible extra platform fee that Shopify adds on top if you use a gateway other than Shopify Payments. If you choose Shopify Payments, the extra platform fee falls away. Our recommendation is always to work through the total cost for your specific payment mix, not just a single fee.
For B2B the picture is more nuanced. Shopify supports partial payments, deposits and splitting payments across an order, which is crucial when customers buy on invoice or on agreed payment terms. This is one of the reasons serious B2B brands often scale up to Shopify Plus.
Integrations: connect Shopify with ERP, inventory and finance
Shopify is strong as a sales platform, but it needs to talk to the rest of the business to deliver real value. The most critical integrations are typically ERP, accounting system, inventory and fulfilment. Can you connect e-conomic to Shopify? Yes, it is done via integration apps or a custom connection, so orders, invoices and payments sync automatically instead of being keyed in manually. The same applies to solutions like Dynamics 365 Business Central, where payments can be reconciled across systems.
The choice is between standard connectors and a custom integration, and it is rarely trivial. A standard app is quick to get started with, but it can become a bottleneck as order volume grows or when your data model deviates from the norm. A custom integration costs more up front but gives you control over error handling, sync logic and scalability. Here is how we typically approach it: we map the data flow end to end before we choose a tool, so the integration matches your actual processes and not the other way around.
Omnichannel: one coherent experience across channels
True omnichannel is about the customer experiencing one business across web, physical store and other channels, while behind the scenes you have a single overview of inventory, orders and customers. By connecting Shopify to a flexible POS system, orders and inventory sync automatically, so an item sold in the store is immediately deducted from what is shown online.
One important point: POS and multichannel features alone do not automatically make your setup true omnichannel if inventory and order data still live in silos. This is where order management, inventory logic and the integration layer become decisive. We recommend treating omnichannel as a data question before a channel question, so you build on a foundation that can scale.
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