In this study, the influence of encapsulation process conditions on the physical properties and chemical composition of encapsulated pumpkin seed oil was investigated. Four variants of encapsulated oil were prepared: spray-dried nonhomogenized emulsions at the inlet temperatures of 180 and 130°C, spray-dried homogenized emulsion at the inlet temperature of 130°C, and freeze-dried homogenized emulsion. The emulsion was prepared by mixing 10.6% oil with 19.8% wall materials (15.9% maltodextrin + 0.5% guar gum + 3.9% whey protein concentrate) and 69.6% distilled water. The quality of encapsulated pumpkin seed oil was evaluated by encapsulation efficiency, surface oil, total oil and moisture contents, flowing properties, color, and size. Additionally, fatty acid composition, pigment characteristics, and the content of bioactive compounds (tocopherols, squalene, and sterols) were determined. Changes of these components after the encapsulation process in comparison to the control pumpkin seed oil were considered as stability parameters. The highest encapsulation efficiency was obtained by spray-drying at the inlet temperature of 130°C. Generally, the spray-drying process had a positive effect upon the physical parameters of encapsulated pumpkin seed oil but results were dependent on process conditions. The higher inlet temperature generated more surface oil, but capsules obtained at the lower temperature were greater in size and more deformed. Although freeze-drying proceeded at a very low temperature, the powder obtained with this technique was characterized by the highest bioactive compound losses (with the exception of sterols) and the lowest stability. The homogenization process applied before spray-drying affected greater polyunsaturated fatty acid, squalene, and pigment degradation. In conclusion, results of the study showed that the spray-drying non-homogenized emulsion was a more recommendable technique for the encapsulation of pumpkin seed oil because of smaller changes of native compounds and better oxidative stability.