Background: This study explores the role of leguminous crops like lima bean in enhancing soil quality and ecosystem stability. Despite existing studies on agronomic aspects, there is a significant research gap on its impact on soil organic matter level, microbial activity, soil health, and nutrient availability. Therefore, this study examines the capacity of lima bean to reactivate soil quality, focusing on its impact on soil organic matter level, microbial activity, soil health, and nutrient availability. Methods: The experimental area was set up in 2023 using three replicates and a randomized block design. Two treatments were used: lima bean-planted plots and control plots with various weeds and without lima bean. Post-harvest soil samples were collected from various agroecological zones and sterilely packed, and physical, chemical, and biological indices were examined. Results: lima bean significantly affected nutrients, enzymes, soil microbial respiration, and other markers. Amylase activity (0.41**) was positively correlated with urease activity (0.73**), while dehydrogenase activity positively correlated with both. Dehydrogenase activity was negatively correlated with total nitrogen (0.66**) and sulfur (0.60**). Lima bean significantly affected soil quality, with all locations showing higher ratings (55–77%) than wild land, except for location D (Ilora). A total of 70% of total nitrogen variation may be attributed to soil quality (r2 = 0.696). Lima bean enhanced soil quality, potentially enhancing productivity and reducing dependence on inorganic nitrogen inputs. Conclusions: The symbiotic relationship between lima bean and nitrogen-fixing bacteria improves nutrient cycling, enhancing agricultural productivity and environmental conservation. Future research should explore the economic viability of integrating lima bean into crop rotations or agroforestry systems for sustainable agricultural practices, providing valuable information for farmers.