Effective equations often provide powerful tools to develop a systematic understanding of detailed properties of a quantum system. This is especially helpful in quantum cosmology where several conceptual and technical difficulties associated with the full quantum equations can be avoided in this way. Here, effective equations for Wheeler-DeWitt and loop quantizations of spatially flat, isotropic cosmological models sourced by a massive or interacting scalar are derived and studied. The resulting systems are remarkably different from that given for a free, massless scalar. This has implications for the coherence of evolving states and the realization of a bounce in loop quantum cosmology.