A survey was conducted from January to March 2023 to assess the soil biological fertility index across five agro-ecological units in the rice-growing belts of Southern Kerala. These units included Onattukara sandy loam (AEU 3), Kari soil (AEU 4), Pokkali soil (AEU 5), Southern laterites (AEU 8), and Midland laterites (AEU 9). The study was carried out in the College of Agriculture, Vellayani Thiruvananthapuram. The survey aimed to assess microbial activity and organic carbon content, thereby enhancing our understanding of the biological fertility across these diverse soil types. Twenty geo-referenced surface soil samples @ 0- 15 cm were collected in every AEU by prescribed method. The collected samples were subjected to the characterization of soil biological properties such as dehydrogenase activity, organic carbon, microbial biomass C, microbial biomass N and soil respiratory rate following the standard protocol. The findings showed that organic carbon in AEU 5 with the highest mean value (3.03 %), followed by AEU 4 (2.19 %), AEU 9 (2.01 %), AEU 8 (1.01 %), and AEU 3 (0.56 %). Dehydrogenase activity was highest in AEU 5 (682.54 µg TPF g-1 hr-1), followed by AEU 4, AEU 9, and AEU 8, and lowest in AEU 3 (76.71 µg TPF g-1 hr-1). AEU 5 exhibited the highest microbial biomass carbon and microbial biomass nitrogen activities, while AEU 8 showed the lowest. Soil respiration was highest in AEU 5 and lowest in AEU 3. Based on these soil microbiological indicators, soils were classified into three categories: low, medium, and high fertility. The Biological Fertility Index (BFI) scores indicated favorable conditions in AEU 4 and 5, moderate in AEU 9, and low in AEU 3 and 8. By establishing a comprehensive understanding of soil biological fertility across various agro-ecological units, the research aims to contribute to improved soil health and crop productivity in the region.