By default, customers see all the payment methods available to them at checkout. This may be inconvenient, especially when you have many payment methods.
The Payment Dependencies add-on allows you to make certain payment methods unavailable, if a customer selects a particular shipping method. In this example we will make Phone ordering the only payment method available for the Custom shipping method.
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Open the Administration panel of your store.
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Go to Administration → Shipping methods.
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Click the name of the shipping method you want to edit (Custom shipping method in our case).
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Scroll down to the Extra section on the shipping method editing page. You’ll see the Allowed payment methods setting.
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Tick the checkboxes of the payment methods you want to allow for the shipping method. In our case we leave only Phone ordering ticked.
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Click the Save button to save your changes.
Now if you try to purchase a product and choose Custom shipping method at checkout, you will only have Phone ordering under Billing options.