The MICROSCOPE experiment was designed to test the weak equivalence principle in space, by comparing the low-frequency dynamics of cylindrical ‘free-falling’ test masses controlled by electrostatic forces. We use data taken during technical sessions aimed at estimating the electrostatic stiffness of MICROSCOPE’s sensors to constrain a short-range Yukawa deviation from Newtonian gravity. We take advantage of the fact that in the limit of small displacements, the gravitational interaction (both Newtonian and Yukawa-like) between nested cylinders is linear, and thus simply characterised by a stiffness. By measuring the total stiffness of the forces acting on a test mass as it moves, and comparing it with the theoretical electrostatic stiffness (expected to dominate), it is a priori possible to infer constraints on the Yukawa potential parameters. However, we find that measurement uncertainties are dominated by the gold wires used to control the electric charge of the test masses, though their related stiffness is indeed smaller than the expected electrostatic stiffness. Moreover, we find a non-zero unaccounted for stiffness that depends on the instrument’s electric configuration, hinting at the presence of patch-field effects. Added to significant uncertainties on the electrostatic model, they only allow for poor constraints on the Yukawa potential. This is not surprising, as MICROSCOPE was not designed for this measurement, but this analysis is the first step to new experimental searches for non-Newtonian gravity in space.