I have Magento 1.9.1 with Paypal Payments Pro (Includes Express Checkout) and Express Checkout. I don't see how to disable those in just one of the stores? When I switch to the Configuration scope for the other store - it does not give me the option to disable it...Any ideas? :-*
How to disable Paypal from just one of the stores in a multi-store setup?
It can be done, but it depends on the way your multi-store is setup.
From the fact that you can't disable the PayPal payment method I conclude that you are running a multi-store setup with storeviews. As far as I know standard Magento functionality does not allow you to disable/enable payment methods on a storeview level.
When your store is configured with multiple websites you should be able to disable/enable payment methods on a per-website level.
Some alternatives based on creating modules are presented here: How to restrict payment methods by store? (https://magento.stackexchange.com/questions/36883/how-to-restrict-payment-methods-by-store) and here: Disable or hide Paypal on specific store view (https://magento.stackexchange.com/questions/61613/disable-or-hide-paypal-on-specific-store-view). I have not tested these approaches though.
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