There are provided systems and methods for smart line routing using wireless beacons. A merchant may set up a wireless beacon throughout a storefront or retail location for the merchant. The beacons may connect to a user's device and provide check-in services to the user. Based on the connections between the user's device and the wireless beacons, information about the user's behavior in the merchant location may be determined. The information may correspond to items/services the user may purchase and an amount of items/services the user may purchase. Using this information and a payment instrument the user utilizes to complete a transaction for the items/services, and expected time for the user to complete a checkout and payment to the merchant may be determined. The expected time can be used to direct the user to a checkout line that minimizes a wait time for each line.