Ethanol extracts of two types of pepper (sweet and hot) were separated into fractions with increasing lipophilicity. After drying the extracts and fractions, their chemical composition, anti-radical activity in the DPPH radical system, and cytotoxic activity against PC-3 and HTC-116 cells were determined. A detailed qualitative analysis of the fractions was performed with the LC-QTOF-MS method. It was found that the chemical composition of pepper fractions did not always reflect their biological activity. The highest antiradical activity was detected in the fraction eluted with 40% methanol from sweet pepper. The highest total content of phenolic compounds was found in an analogous fraction from hot pepper, and this fraction showed the strongest cytotoxic effect on the PC-3 tumour line. The LC-MS analysis identified 53 compounds, six of which were present only in sweet pepper and four only in hot pepper. The unique chemical composition of the extracts was found to modulate their biological activity, which can only be verified experimentally.