Crop residue incorporation generally improves long-term soil quality. However, it may have temporary negative environmental and agronomic effects in anaerobic rice soils, such as greenhouse gas production, release of allegedly phytotoxic organic acids into soil solution, and immobilization of nutrients. The straw from a brittle stem mutant of rice (Oryza sativa L. var. IR68) was observed to break into smaller pieces during threshing as compared with the non-brittle phenotype. To test the hypothesis that brittle straw would decompose faster due to different breakage patterns during threshing and to chemical composition differences, decomposition rates of the two phenotypes were compared in litter bag and pot incubation studies with respect to the three problems above. The brittle mutant decomposed faster, as indicated by higher levels of methane and organic acid production, but did not show a significant difference in N immobilization timing. With proper water management to minimize methane formation, the use of the brittle stem mutant could potentially enable a shorter fallow period between crops in rice-rice cropping systems.