Stink bean, Parkia speciosa, is recognized as a significantly underutilized legume with versatile utility and diverse benefits. However, information on the impact of different processing methods, such as germination and hydrothermal cooking, is scarce on stink beans (SBs). Therefore, the current research aimed to explore the efficacy of germination (G) and hydrothermal cooking (HTC) on the physiochemical properties, proximate composition, techno-functional properties, and antioxidant potential of SB flour. Furthermore, Fourier transform infrared spectroscopy (FTIR) and field emission scanning electron microscopy (FESEM) were employed to assess structural and morphological changes. The results revealed that the physiochemical properties of SB were significantly enhanced through processing, with more pronounced improvements observed during germination. Additionally, SBG exhibited a significantly higher protein content and lower fat content compared to SBHTC and stink bean raw (SBR). Moreover, techno-functional properties such as color intensity, least gelation concentration, and pasting properties were significantly improved in SBG compared to SBHTC and SBR. FTIR analysis of SBG and SBHTC indicated structural modifications in the lipid, protein, and carbohydrate molecules. FESEM examination revealed morphological changes in SBG and SBHTC when compared to SBR. Importantly, SBG exhibited higher antioxidant activity and total phenolic content in comparison to SBHTC and SBR. Therefore, processed SB flour can be incorporated and utilized in product development, highlighting its potential as a plant-based protein source for protein-rich breakfast bars and cookies.