Land use effect of tropical Andosol, with two from crop lands (Site 1 and Site 2) and one from Agroforestry coffee plantation (Site 3) was explored under laboratory conditions to understand their physical, chemical and biological properties and soil organic carbon (SOC) stocks from the rift valley of Ethiopia. Site 3 that acquired less cultivation than others exhibited better aggregate size fraction (AF, 55%), higher aggregate stability (AS, 91%), and greater active microbial biomass (AMB), reflecting better soil structure development. Comparatively, higher total carbon (TC), organic carbon (OC) and total nitrogen (TN) concentrations were recorded in bulk soils and microaggregate fractions of Site 2 and Site 3 than in intensively cultivated Site 1. As expected, microaggregate fractions displayed greater OC and TN than bulk soils across all land uses. Site 1 revealed higher metabolic quotient (qCO₂) and lower SOC stock (2.1 Mg·ha^-1), suggesting microbial stress, while micro nutrients deficiencies were observed with the alkaline soil (Site 2). Conversely, the highest SOC stock was exhibited with Site 3 (4.2 Mg·ha^-1), indicating the importance of coffee land use in C sequestration. Crop lands, depleted much of their native carbon stocks had significant CO₂ sink capacity. Hence, management practices that increase the input of organic resources should be adopted to build SOM and enhance soil fertility.