Once the temperature of a bosonic gas is smaller than the critical, density dependent, transition temperature, a Bose -Einstein Condensation process can take place during the cosmological evolution of the Universe. Bose -Einstein Condensates are very strong candidates for dark matter, since they can solve some major issues in observational astrophysics, like, for example, the galactic core/cusp problem. The presence of the dark matter condensates also drastically affects the cosmic history of the Universe. In the present paper we analyze the effects of the finite dark matter temperature on the cosmological evolution of the Bose-Einstein Condensate dark matter systems. We formulate the basic equations describing the finite temperature condensate, representing a generalized Gross-Pitaevskii equation that takes into account the presence of the thermal cloud in thermodynamic equilibrium with the condensate. The temperature dependent equations of state of the thermal cloud and of the condensate are explicitly obtained in an analytical form. By assuming a flat Friedmann-Robertson-Walker (FRW) geometry, the cosmological evolution of the finite temperature dark matter filled Universe is considered in detail in the framework of a two interacting fluid dark matter model, describing the transition from the initial thermal cloud to the low temperature condensate state. The dynamics of the cosmological parameters during the finite temperature dominated phase of the dark matter evolution are investigated in detail, and it is shown that the presence of the thermal excitations leads to an overall increase in the expansion rate of the Universe.