This research compared the effects of vacuum freeze drying (VFD) and conventional freeze drying (CFD) processes on the stability of fish oil–loaded nanocapsules (NCs). For CFD, the showed aggregation that was dependent on the freezing temperature. The encapsulation efficiency of CFD was greater than that of VFD, except at the freezing temperature of 30C. From differential scanning calorimetry (DSC) analysis and scanning electron microscopy (SEM) and transmission electron microscopy (TEM) images, it was concluded that the CFD process was more effective in the oxidative stability of the fish oil–loaded NCs. In addition, the vacuum-freezing process may affect the fragility of the poly-e-caprolactone membrane due to its low encapsulation efficiency and aggregation of particles. No differences in Z- potential values between the CFD samples were observed, whereas in the VFD samples, it became increased in the negative charge when decreasing the cooling temperature of the fish oil–loaded nano-capsules for the freeze-drying procedure. Regarding the observation of surface tension, CFD samples presented lower values than VFD samples at given freezing temperature.