Traditional pasteurization (PT), using high temperatures and long process times, can determine significant degradation of bioactive compounds, so research into other methods of preserving fruit products is needed. Strawberry-chokeberry (SC) and strawberry-blackcurrant (SB) nectars were preserved by PT (90°C/10 min), HTST (90°C/15 s) and UHT (130°C/5 s) methods and stored for 6 months under refrigeration. Before this study was performed, the used parameters of HTST and UHT had not been identified in the literature. Qualitative and quantitative analyses of phenolic compounds by the UPLC-PDA-QTOF/MS method were carried out. In total, 23 phenolic compounds in SC and 21 in SB were identified (anthocyanins, flavan-3-ols, phenolic acids and their hexosides, flavonol glycosides). Considering the sum of all identified compounds, there was a decrease of 12%, 1% and 6% in SC after PT, HTST and UHT, respectively, while in SB, there was a decrease of 14% and 10% after PT and UHT, and no significant change after HTST. Taking into account storage, most of the compounds were partially degraded, while in the case of flavan-3-ols, an increase of 26-128% (depending on the nectar and method) was observed after 6 months of storage. At the end of the storage period following PT, HTST and UHT, the sum of identified compounds in SC decreased by 13%, 21% and 20%, respectively, while in SB, decreases of31%, 40% and 41% were reported. HTST and UHT-preserved nectars had more bioactive compounds than PT-preserved samples after 6 months of storage. HTST was the best preservation method as it allowed the highest retention of bioactive components.