If your customers are allowed to pick their orders up from your warehouse or physical store, then you can still use Shipmondo for handling this flow. You can fulfill the order and mark it as Picked up.
This is how you can do that
When you've packed your order, you need to create a fulfillment for it the same way you would if the order was supposed to be sent to the customer.
Click on the Create fulfillment > Create.
When the customer has picked up their order and you've captured payment, you can change the order status from Packed to Picked up, as shown below.
Your order will thus be registered as complete in Shipmondo.