BACKGROUND: Monascus pigments (MPs) produced by the genus Monascus, have been utilized for more than 2000 years in the food industry. In the present study, by submerged batch-fermentation (SBF), we were able to obtain a mutant strain with a high tolerance of inhibitory compounds generated from rice husk hydrolysate, allowing the production of MPs.RESULTS: The mutant strain, M. Purpureus M523 with high rice husk hydrolysate tolerance was obtained using the atmospheric and room temperature plasma (ARTP) screening system, producing 39.48 U mL −1 extracellular total MPs (yellow and orange MPs), using non-detoxified rice husk diluted sulfuric acid hydrolysate (RHSAH) as the carbon source in SBF. Extracellular MPs (exMPs) production was enhanced to 72.1 and 80.7 U mL −1 in supplemented SBF (SSBF) and immobilized fermentation (IF) using non-detoxified RHSAH, with productivities of 0.16 and 0.37 U mL −1 h −1 , respectively. In addition, our findings revealed that despite having a high RHSAH tolerance, the mutant strain was unable to degrade phenolic compounds. Furthermore, we discovered that inhibitory compounds, including furfural (Fur) and 5 0 -hydroxymethyl furfural (5 0 -HMF), not only inhibit MP biosynthesis, but also regulate the conversion of pigment components.CONCLUSION: The low-cost agricultural by-product, rice husk, can serve as an efficient substitute for MP production with high productivity via IF by Monascus spp.