Rice lipids are usually stable in the intact spherosomes in the cell. However, lipid membrane destruction by the phospholipase, physical injury or high temperature, initiates hydrolysis through the action of lipases. Further, microbial related lipolysis demands simultaneous antimicrobial and antioxidation control to stabilize lipids. Accordingly, the activity of volatiles from polar extract (AEPE), non-polar extracts (MCPEV and HEPEV) and crude sample (CRUPV) of propolis on rice bran and brown rice (Oryza sativa, hinohikari var.) quality was evaluated. We comprehensively investigated treatment effects on three major rice lipids and elucidated through microscopic morphological observation and genotype analysis of the 16S ribosomal DNA the fungal and bacterial distribution on the product respectively. Oleic, linoleic and palmitic acids composition in brown rice was affected by the treatments. HEPEV treated brown rice indicated lowest stabilization of the fatty acids, albeit marginally greater than the control. The stabilization strength was such: CRUPV> AEPEV> MCPEV>HEPEV. This pattern was not replicated regarding the composition of fatty acids in the bran layer only. The bacterial species of Bacillus genus were most predominant with Bacillus cereus persistently on all samples and Moraxella osloensis, Pseudomonas oleovorans, Sphingomonas paucimobilis, Xanthomonas campestris, Curtobacterium citreum, Curtobacterium flaccumfaciens and Aerococcus viridans affecting the samples discriminately. Penicillium spp. was the most dominant fungi and persisted in all the treatments. However, MCPEV and CRUPV treatments indicated the lowest species infestation numbers. Post treatment milling of pretreated grain revealed improved head rice for MCPEV and CRUPV treatments. Improved end product whiteness was only noticeable by MCPEV treatment.