Coffee productions should have environmental values such as providing high soil microbial diversity while producinghigh yield. To examine that purposes, two experimental plots were constucted at benchmark site of Conservationand Sustainable Management of Below-Ground Biodiversity (CSM-BGBD), in Sumberjaya Subdistrict, WestLampung, Indonesia, during 2007-2010. Types of coffee agro-ecosystem to be examined were Coffea canephorawith shade trees of Gliricidia sepium, Erythrina sububrams, Michelia champaca, and no shade. Two plots wereconstructed at 5-years-coffee and 15-years-coffee. Diversity of soil bacteria was determined based on DNA fingerprinting of total soil bacteria using Ribosomal Intergenic Spacer Analysis (RISA) method. The results showed that:(1) For mature coffee (15 years old), shade-grown coffee agro-ecosystems had higher soil bacterial diversity thanthose of no shade coffee agro-ecosystem, (2) Shaded coffee agro-ecosystems were able to conserve soil bacterialdiversity better than no-shade coffee agro-ecosystem. Soil organic C and total litter biomass had positive effect onsoil bacterial diversity, (3) Types of agro-ecosystem significantly affected the bean yield of 15 years coffee. Coffeeagro-ecosystems shaded by legume trees had higher yield than those of non-legume shade and no shade coffeeagro-ecosystem, (4) Shannon-Weaver indices of soil bacterial diversity together with weed biomass and N contentof coffee leaf had positive effect on coffee bean yield.