This study explores the enhancement of Cucumis momordica seed powder's properties through Eurotium cristatum-mediated solid-state fermentation (SSF) and its application in nanoemulsions, emphasizing protein content, functional properties, stability, and antimicrobial activity. The protein content increased significantly from 23.28±0.23 % in the control to 29.83±0.12 % after 144 h of fermentation. The Cucumis momordica seed powder fermented for 96 h was further analyzed for its functional properties and characterization. The water absorption capacity was increased from 0.91 to 2.56 g/g, and oil absorption capacity from 0.79 to 1.16 g/g. SEM and FTIR analyses revealed morphological changes and chemical profile alterations, indicating enzymatic degradation and enhanced functional properties. Nanoemulsions from fermented powder showed reduced droplet sizes (148±0.34 nm to 126±0.37 nm) and more negative zeta potentials (-24.5±0.12 mV to −25.79±0.18 mV), suggesting improved stability. Temperature stability was superior in fermented seed powder nanoemulsions, demonstrating enhanced thermal resistance. Antimicrobial tests against E. coli and S. aureus showed significantly lower MIC and MBC values for fermented powder nanoemulsions (E. coli MIC: 1.089 mg/mL, MBC: 2.189 mg/mL; S. aureus MIC: 0.459 mg/mL, MBC: 1.196 mg/mL), indicating increased antimicrobial efficacy. These results highlight the potential of SSF and nanoemulsion technology in advancing the functionality and application of Cucumis Momordica seeds as natural antimicrobial agents.