The initial value problem of scalar-tensor theories of gravity (STT) is analyzed in the physical (Jordan) frame using a 3+1 decomposition of spacetime. A first order strongly hyperbolic system is obtained for which the well posedness of the Cauchy problem can be established. We provide two simple applications of the 3+1 system of equations: one for static and spherically symmetric spacetimes which allows the construction of unstable initial data (compact objects) for which a further black hole formation and scalar gravitational wave emission can be analyzed, and another application is for homogeneous and isotropic spacetimes that permits to study the dynamics of the Universe in the framework of STT.