Coffee production in the Caribbean and Latin America is an important commodity in terms of economic, ecological and social value. Coffee production in Puerto Rico was intensified in the 1960s, with a shift to higher-yield varieties, increased use of pesticides and fertilizers, increased mechanization, higher-density planting patterns, with production under full sunlight. There is concern that long-term, intensive coffee production under full sunlight may have a negative impact on agroecosystem sustainability. Soil physical, chemical and biological attributes from representative major coffee production regions in Puerto Rico under partial shade and full sunlight were quantified. Soils from secondary forests at least 25 years old were included for comparison. Soil fertility differed between forest and coffee agroecosystems with favorable soil reaction, improved nutrient reserves and availability in forested systems; coffee under shade had a tendency towards improved soil fertility. The soil physical structure was significantly affected by coffee production, with a greater proportion of large macroaggregates in forested sites than in coffee agroecosystems. Coffee under both partial shade and full sunlight had a lower proportion of macroaggregates and a higher proportion of microaggregates which may have important implications for the capacity of soils under coffee production to store C and release Ν for crops. Soil organic carbon and nitrogen, microbial biomass and fungal groups were negatively affected by coffee production, with few observed differences between coffee under shade and full sunlight. The soil biological community structure was negatively influenced by coffee production relative to secondary forested sites, with coffee under shade having slight improvement relative to coffee under sun.