We investigate how the temperature calculated from the microcanonical entropy compares with the canonical temperature for finite isolated quantum systems. We concentrate on systems with sizes that make them accessible to numerical exact diagonalization. We thus characterize the deviations from ensemble equivalence at finite sizes. We describe multiple ways to compute the microcanonical entropy and present numerical results for the entropy and temperature computed in these various ways. We show that using an energy window whose width has a particular energy dependence results in a temperature with minimal deviations from the canonical temperature.