Considerable attention has been paid to exploring the biotechnological applications of several Monascus sp. for pigment production. In this study, our focus is on enhancing the bioprocessing of red pigment (RP) derived from the endophytic fungus Monascus ruber SRZ112. To achieve this, we developed a stable mutant strain with improved productivity through gamma irradiation. This mutant was then employed in the immobilization technique using various entrapment carriers. Subsequently, we optimized the culture medium for maximal RP production using the Response Surface Methodology. Finally, these immobilized cultures were successfully utilized for RP production using a semi-continuous mode of fermentation. After eight cycles of fermentation, the highest RP yield by immobilized mycelia reached 309.17 CV mL−1, a significant increase compared to the original titer. Importantly, this study marks the first report on the successful production of Monascus RP in a semi-continuous mode using gamma rays’ mutant strain, offering prospects for commercial production.