In this work, the impact of cation disorder on the electrical properties of biaxially textured Co2ZnO4 and Co2NiO4 thin films grown by pulsed laser deposition are investigated using a combination of experiment and theory. Resonant elastic X-ray diffraction along with conductivity measurements both before and after post-deposition annealing show that Co2NiO4 and Co2NiO4 exhibit opposite changes of the conductivity with cation disorder, which can be traced back to their different ground-state atomic structures, being normal and inverse spinel, respectively. Electronic structure calculations identify a self-doping mechanism as the origin of conductivity. A novel thermodynamic model describes the non-equilibrium cation disorder in terms of an effective temperature. This work offers a way of controlling the conductivity in spinels in a quantitative manner by controlling the cation disorder and a new design principle whereby non-equilibrium growth can be used to create beneficial disorder.