Topographic images of [Fe(Htrz)₂(trz)](BF₄) nanoparticles were acquired across the first-order spin transition using variable-temperature atomic force microscopy (AFM) in amplitude modulation mode. These studies revealed a complex morphology of the particles consisting of aggregates of small nanocrystals, which expand, separate and re-aggregate due to the mechanical stress during the spin-state switching events. Both reversible (prompt or slow recovery) and irreversible effects (fatigue) on the particle morphology were evidenced and correlated with the spin crossover properties.