There are provided systems and methods for intelligent selection of transaction processing technology available at a merchant location. A user may visit a merchant location and desire to purchase items from the merchant at the merchant location. The user may have options for one or more payment instruments to use at the merchant location, including payment applications with a mobile communication device. A payment provider may detect the location of the user and determine that the user's location matches the merchant's location through a geo-fenced area for the merchant. The payment provider may then configure a payment process for the user to utilize at the merchant location using payment mechanisms accepted at the merchant location. Where multiple merchants are located nearby, the payment provider may utilize additional known information for the user to select the most likely merchant for the user.