Mastering the nanostructuration of molecular materials onto solid surfaces and understanding how this process affects their properties are of utmost importance for their integration into solid-state electronic devices. This is even more important for spin crossover (SCO) systems, in which the spin transition is extremely sensitive to size reduction effects. These bi-stable materials have great potential for the development of nanotechnological applications provided their intrinsic properties can be successfully implemented in nanometric films, amenable to the fabrication of functional nanodevices. Here we report the fabrication of crystalline ultrathin films (<1-43 nm) of two-dimensional Hofmann-type coordination polymers by using an improved layer-by-layer strategy and a close examination of their SCO properties at the nanoscale. X-ray absorption spectroscopy data in combination with extensive atomic force microscopy analysis reveal critical dependence of the SCO transition on the number of layers and the microstructure of the films. This originates from the formation of segregated nanocrystals in early stages of the growth process that coalesce into a continuous film with an increasing number of growth cycles for an overall behaviour reminiscent of the bulk. As a result, the completeness of the high spin/low spin transition is dramatically hindered for films of less than 15 layers revealing serious limitations to the ultimate thickness that might be representative of the performance of the bulk when processing SCO materials as ultrathin films. This unprecedented exploration of the particularities of the growth of SCO thin films at the nanoscale should encourage researchers to put a spotlight on these issues when contemplating their integration into devices.