The volcanoclastic mountains of Central America offer elevations ideal for coffee production. Both vulcanism and land use can have significant impacts on soil formation and properties. We evaluated how the interactive impacts of soil formation and coffee-dominated land use modulate soil storage and vertical distribution of organic carbon and nutrient elements in a volcanically active landscape dominated by coffee agriculture in south-central Guatemala. Thirty-seven pedons under coffee production (n = 29), forest cover (n = 5) and pasture (n = 3) were characterized and classified, and concentrations and stocks of organic carbon and macronutrient and micronutrient elements were quantified across genetic horizons. Additionally, soil organic carbon (SOC) stock values calculated using the fixed depth (FD) and equivalent soil mass (ESM) methodologies were compared. The active stratovolcano in the region had a strong effect on the development of andic properties and soil horizon burial, with thirty-one pedons classified as Andisols, three as Inceptisols and three as Entisols. Land use management practices and soil horizon burial by deposition of volcanic material were partly reflected in the vertical distribution of SOC concentrations and stocks. The vertical distribution of macronutrients was generally more sensitive to land use than the vertical distribution micronutrients, which could potentially reflect differences in inputs via fertilizers and vegetation cover and in outputs with biomass harvest. Soil organic carbon stocks were similar when calculated by FD and ESM, reflecting relatively consistent depth-wise bulk density. These results demonstrate that in volcanically active landscapes, land use should be considered in concert with soil-forming factors to comprehensively understand organic carbon and nutrient element storage in soils.