Drivers of nitrogen (N) mineralization in paddy soils, especially under anaerobic soil conditions, are elusive. The influences of exogenous organic matter (OM) and fertilizer application on the activities of five relevant enzymes (β-glucosaminidase, β-glucosidase, L-glutaminase, urease and arylamidase) were measured in two long-term field experiments. Of the two field experiments, the 18-year field experiment was established in a weathered terrace soil with rice-wheat crop rotation at the Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU) farm with five OM treatments and two levels of mineral N fertilizer. The 30-year experiment was established in a young floodplain soil with rice-rice crop rotation at the Bangladesh Agricultural University (BAU) farm with five mineral fertilizer treatments including one with farm yard manure. At BSMRAU, N fertilizer and OM amendments significantly increased all enzyme activities, suggesting the availability of primarily substrate for microbial activity. Whereas at BAU, non-responsiveness of β-glucosidase activity, suggesting that fertilizer and OM amendments had little effect on overall soil microbial activity. Nevertheless the microbial demand for N, β-glucosaminidase and L-glutaminase activities differed among the treatments (P < 0.05) and showed opposite trends with soil N mineralization. Hence enzymatic pathways to acquire N differed with the treatment at BAU site, indicates differences in soil N quality and bio-availability. L-glutaminase activity was the sole investigated variable that positively correlated to both the aerobic and anaerobic N mineralization rates in both field experiments. Combined with a negative correlation between β-glucosaminidase activity and N mineralization rate, it appears that terminal amino acid NH2 hydrolysis was a rate-limiting step for soil N mineralization at the BAU site. Future investigations with joint quantification of polyphenol accumulation and binding of N alongside an array of extracellular enzymes, including oxidases for phenols and hydrolases for N-compounds, would enable verification of the hypothesized binding and stabilization of N with accumulating polyphenols at BAU site under SOM storing management.