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Is there a way that I can trigger a payment gateway to process an order that has already been processed already.

i.e. A user selected to pay for an order using the manual payment method and process their order as such. The user then decides to contact the site admin because they instead wish to for this order via another payment gateway.

Is there a way using php that I can allow this to happen and if so where do I look to find the correct methods that will achieve this.

Thanks

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In that scenario, no. If the user has selected a payment method and completed the checkout using that payment method then the easiest thing would be to cancel that order and run through another one with the change of payment method.

In other circumstances when you don't want to take payment immediately you can set the Credit Card Payment Method to Authorize Only in Store > Settings > General. This will allow you to take the payment manually at a later date.

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You will need to check with your payment gateway how long you can keep an authorised payment open before needing claim. This can vary between payment gateways and you will usually need to manually capture within a matter of days or the order will be dropped.

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