A nanocapsule (NC)–gelatin suspension was freeze-dried to produce a sample of dry food. The obtained dried product was rehydrated, and the dispersibility of the nanocapsules was investigated. It was found that the prepared freeze-dried food had different dispersion characteristics at different positions in the dried bulk sample, and this heterogeneity was dependent on the cooling program used during the processing. A model mathematical calculation was carried out in order to obtain the thermal profiles of the sample during freezing. The freezing front velocity and the viscosity of the solution at/around the freezing front were estimated by using the simulated thermal profiles. The dispersibility of the prepared dry food was found to correlate with these values. This suggested that the gel network formation of NC–gelatin would be advantageous for producing excellent NC dispersion characteristics after drying. A slow cooling condition is favourable for promoting sol–gel transition in the solution. However, the large scale of ices formed during slow freezing would damage the gel networks, leading to poor dispersibility. The present work discusses key processing factors for controlling the dispersion characteristics of nanocapsules stabilized in a freeze-dried food sample.