Thin films of the molecular spin‐crossover complex [Fe(HB(1,2,4‐triazol‐1‐yl)3)2] undergo spin transition above room temperature, which can be exploited in sensors, actuators, and information processing devices. Variable temperature viscoelastic mapping of the films by atomic force microscopy reveals a pronounced decrease of the elastic modulus when going from the low spin (5.2 ± 0.4 GPa) to the high spin (3.6 ± 0.2 GPa) state, which is also accompanied by increasing energy dissipation. This technique allows imaging, with high spatial resolution, of the formation of high spin puddles around film defects, which is ascribed to local strain relaxation. On the other hand, no clustering process due to cooperative phenomena was observed. This experimental approach sets the stage for the investigation of spin transition at the nanoscale, including phase nucleation and evolution as well as local strain effects.