Spin-crossover particles of [Fe(Htrz)2trz](BF4) with sizes of some hundred nanometers are studied by in situ electron microscopy. Despite their high radiation sensitivity, it was possible to analyze the particles by imaging and diffraction so that a detailed analysis of crystallographic defects in individual particles became possible. The presence of one or several tilt boundaries, where the tilt axis is the direction of the polymer chains, is detected in each particle. An in situ exposure of the particles to temperature variations or short laser pulses to induce the spin crossover shows that the defect structure only changes after a high number of transformations between the low-spin and high-spin phases. The observations are explained by the anisotropy of the atomic architecture within the crystals, which facilitates defects between weakly linked crystallographic planes.