Coffee cultivation is essential for tropical agriculture and rural livelihoods in Latin America, Africa, and Asia. However, coffee production in tropical low-altitude regions characterized by acidic soils and elevated temperatures faces significant challenges, and the soil microbiological dynamics under these environments remain poorly understood. This study assessed the impact of agricultural practices and edaphoclimatic variables on soil biological indicators, such as enzymatic activities and basal respiration in coffee fields located below 1000 m altitude in Colombia. Surveys conducted with 40 coffee growers characterized various agronomic practices and socioeconomic factors, and 150 soil samples were collected from their coffee crops of differing ages and associated species. Enzymatic activities were measured using specific substrates, including acid and alkaline phosphatase, arylsulfatase, urease, dehydrogenase, and ß-glucosidase. Statistical analyses including constrained ordination, Spearman correlations, and mixed models, were employed to evaluate variations in biological indicators concerning agronomic practices and edaphoclimatic conditions. Four groups of coffee growers were identified based on their management practices. Livestock-focused growers who utilized organic fertilizers exhibited the highest enzymatic activity, with measurements of acid phosphatase at 365 µg g-1 h-1, alkaline phosphatase at 49 µg g-1 h-1, and arylsulfatase at 137 µg g-1 h-1. In contrast, traditional growers with older plantations recorded the lowest acid phosphatase (215 µg g-1 h-1), alkaline phosphatase (36 µg g-1 h-1), and ß-glucosidase (30 µg g-1 h-1). Basal soil respiration was significantly higher in shade-grown coffee compared to sun-grown (43.0 and 12.6 mg CO2–C kg-1 soil d-1, respectively). Coffee intercropping with Musaceae, Cocoa, and Inga species, organic fertilization, and liming enhanced soil biological indicators.