Since thermal treatment of ready-to-eat sprouts is suggested in order to obtain microbiologically safe sprouts, changes in bioactive compound levels in rapeseed and radish sprouts, after pasteurization and sterilization, were addressed in this study. The seeds of double low rapeseed (Brassica napus L. oleifera.) and radish (Raphanus sativus L. major) after four days of germination were collected and subjected to thermal treatment, including pasteurization (95°C/30 min) and sterilization (1.5 atm/30 min). The following bioactive compounds were analysed before and after the thermal treatment of sprouts: tocopherols (α-T, β-T, γ-T, δ-T), glucosinolates (GLS), total phenolic compounds (TPC), and reduced glutathione (GSH). The trolox equivalent antioxidant capacity (TEAC) of thermally-treated sprouts was compared to that of the ready-to-eat ones. The results showed that after the thermal treatment the content of all tocopherols decreased drastically in the investigated rapeseed and radish sprouts. The pasteurization of rapeseed and radish sprouts caused a decrease in the content of all aliphatic, indolic and aryl GLS (present only in rapeseed). The heat treatment via sterilization caused greater decreases in the above-mentioned groups of GLS when compared to the pasteurization. Both thermal treatment processes were found to determine the content of TPC. In the case of rapeseed sprouts only, a small decrease was noted, however an increase was found in respect to radish sprouts. A decrease in TEAC of thermally-treated rapeseed and radish sprouts was observed. Among the compounds investigated in this study, only the amount of GSH found in the heat treated sprouts was at least two- or threefold higher when compared to the untreated sprouts. Thermal processes used in this study were observed to negatively interact with some biologically active compounds present in the investigated sprouts, hence a need of the search for another method for fresh sprouts preservation was postulated.