Cruciferous vegetables represent a valuable source of bioactive compounds. However, there is currently a deficiency of information regarding the extent to which these compounds remain bioaccessible to the body following thermal treatment and digestion processes within the digestive tract. Accordingly, the aim of this study was to evaluate the impact of heat treatment and in vitro digestion on the level of selected bioactive compounds in Brussels sprouts. The Brussels sprouts samples were subjected to a range of thermal processing techniques, which were then followed by a simulated in vitro digestion. The investigated compounds were analyzed using UV-Vis spectrometry and liquid chromatography coupled with mass spectrometry (LC-MS). The findings revealed that the sous-vide method of cooking Brussels sprouts resulted in significantly higher losses of glucosinolates (GLS) in comparison to conventional cooking methods. No significant differences were observed with regard to isothiocyanates and indoles. The analysis of GLS following digestion revealed that the process was more effective after sous vide and traditional cooking, and slightly less effective after steam cooking. With regard to individual compounds, glucoraphanin (GRA), glucoraphenin (GIV), and gluconasturtiin (GNS) were found to be completely degraded, whereas methoxyglucobrassicin (metGBS) was the most resistant to digestion in both the sous vide and steamed Brussels sprouts. The results indicated that the process of simulating digestion had no significant impact on isothiocyanates and indoles. This suggests that, if present in the heat-treated samples, these compounds remained stable during the in vitro digestion procedure.