Amorphous CdSe nanoparticles were prepared by a base-catalyzed room-temperature reaction between cadmium nitrate and selenourea, with dodecanethiol as a capping ligand. The nanoparticle size could be controlled from 1.9 to 3.6 nm by increasing the water concentration in the reaction. When the nanoparticles were heated in a pyridine suspension, excitonic peaks appeared in the initially featureless optical absorption spectra. By changing the suspension solvent and the capping ligand and its concentration, it was shown that the dynamic surface exchange between the ligand and pyridine controls the crystallization process. This phenomenon was interpreted as a surface rigidity effect imposed by the ligand, whose importance was separately evidenced on the dried nanoparticles by the evolution of X-ray diffraction patterns and Raman spectra. In particular, both techniques showed that a threshold temperature is needed before crystallization occurs, and such a threshold was related to ligand desorption. The surface effect was directly visualized by high-resolution transmission electron microscopy observations of the amorphous particles, where crystallization under the electron beam was observed to start by the formation of a crystalline nucleus in the nanoparticle interior and then to extend to the whole structure.