The effect of treatment of pepper fruits with gaseous ozone and storage time following the ozonation process on changes in the content of lipophilic fraction is analyzed for the first time in this paper. The aim of the present study was to assess the impact of ozone treatment on the composition of lipophilic compound fraction and its antioxidant activity (AA). Pepper fruits of cv. Cyklon were ozonated for 1 and 3 h immediately after harvesting. Then, the fruits were stored for 30 days under refrigeration conditions. The total content of phenolic compounds and the AA of the lipophilic fraction isolated from the pericarp and placenta of the fruits were investigated after 10, 20, and 30 days of storage. Additionally, quantitative high-performance liquid chromatography diode array detection analysis of individual phenolic compounds was performed. The results revealed that the content and activity of secondary metabolites varied during storage, with the highest values recorded on the 20th day after harvest, both in control and ozonated fruits, regardless of the ozone dosage used. Treatment of the fruits with ozone for 3 h, but not for 1 h, exhibited a positive effect on the phenolic composition and AA during the prolonged storage of pepper fruits. Three hours of ozonation seems to be the appropriate time to increase the persistence of pepper fruits during storage.