The growing focus on environmental sustainability and global demand for nutritious foods has spurred research on utilizing bioactive compounds from the food industry by-products. Muskmelon seeds, often overlooked, contain valuable phytochemicals such as phenolics, saponins, alkaloids, and polyunsaturated fatty acids. This study explores the drying of muskmelon seeds, unveiling the potential for preserving these bioactive compounds. Muskmelon seeds were dried in a tray dryer at temperatures ranging from 40 °C to 60 °C, with close monitoring and recording of their moisture content. The recorded data was transformed into moisture ratios and analyzed using various semi-theoretical mathematical models to comprehend the drying kinetics and behavior of the process. The models were compared using the coefficient of determination (R2) and chi-square test (X2). A substantial reduction in drying times (450–240 min) and increase in diffusivity values (4.8 × e−11m2/s to 9.03 × e−11m2/s) was observed as the temperature increased from 40 °C to 60 °C. An activation energy of 27.317 kJ/mol was observed, and the Page model emerged as the best fit (R2 = 0.99; X2 = 4.20 × 10–4). High retention of bioactive compounds was observed in dried seeds, and hence these can be used to develop functional foods or dietary supplements.