There are provided systems and methods for automatic synchronization of a device for transaction processing based on geo-fenced locations. A merchant may geo-fence an area corresponding to the merchant's location where a user may visit to purchase an item. The merchant may provide multiple transaction processing and payment options 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 the 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.