In recent years, several plant-based biofules including the oil-seed crops are explored as alternate sources of fuels, that could potentially produce huge quantities of oil extracted seed meals. A microcosm experiment was conducted to evaluate biofuel oilseed meals of mustard (Brassica juncea) and flax (Linum usitatissimum) as soil amendments and their impact on soil pH, nitrogen mineralization and microbial populations. Two soils were used for this study, one was a low pH clay soil and the other a high pH sandy soil, which were seperately amended with 1% (W/W) of the seed meals and were incubated for 3 months.  Both mustard and flax seed meals significantly reduced the soil pH in high pH sandy soil (from 8.0 to around pH 7.0), but only slightly decreased the pH in low pH clay soils. Nitrogen was readily minerlized in both mustard and flax amendments. Nitrate concentrations in mustard amended high pH soils were slightly lower until 14d, compared to flax amended; but there were no significant differences between the treatments later on. Isothiocyanates originating from the mustard seed meal were detected in soils, but persisted only until 3-7 days, which might have inhibited microbial nitrification during the first week of incubation. Microbial communities were significantly different between mustard and flax seed meals amended soils.