The purpose of this paper is to describe geometrically discrete Lagrangian and Hamiltonian Mechanics on Lie groupoids. From a variational principle we derive the discrete Euler-Lagrange equations and we introduce a symplectic 2-section, which is preserved by the Lagrange evolution operator. In terms of the discrete Legendre transformations we define the Hamiltonian evolution operator which is a symplectic map with respect to the canonical symplectic 2-section on the prolongation of the dual of the Lie algebroid of the given groupoid. The equations we get include as particular cases the classical discrete Euler-Lagrange equations, the discrete Euler-Poincaré and discrete Lagrange-Poincaré equations. Our results can be important for the construction of geometric integrators for continuous Lagrangian systems.This work has been partially supported by MICYT (Spain) Grants BMF 2003-01319, MTM 2004-7832 and BMF 2003-02532.Peer reviewed