Abstract The problem of penetrative convection in a fluid saturated porous medium heated internally is analysed. The linear instability theory and nonlinear energy theory are derived and then tested using three dimensions simulation. Critical Rayleigh numbers are obtained numerically for the case of a uniform heat source in a layer with two fixed surfaces. The validity of both the linear instability and global nonlinear energy stability thresholds are tested using a three dimensional simulation. Our results show that the linear threshold accurately predicts the onset of instability in the basic steady state. However, the required time to arrive at the basic steady state increases significantly as the Rayleigh number tends to the linear threshold.