Stable soil aggregates and high microbial diversity are essential for efficient nutrient recycling in soil. This study evaluated effects of different arable land-use systems on soil aggregation and associated composition and total diversity of bacteria and fungi. For this purpose, 5- and 3-year-old field trials were selected, two in sub-humid (orthic Acrisols and oxidic Ferralsols) and one in semi-arid (chromic Cambisol) region in Kenya. The treatments included combinations of tillage (conventional tillage [CT] and reduced tillage [RT]), crop residue management (0 and 2 t ha?1 maize stover) and cropping systems (continuous maize, maize-soybean intercropping and rotation) in the sub-humid sites, and of different tillage (CT, no-till and tied-ridging) and organic fertilization management (manure and crop residue) in semi-arid Kenya. The innovativeness of this study is the research in tropical soils where the concept of aggregate hierarchy is not generally accepted yet. The results showed that aggregate mean weight diameter (MWD) at 0-15 cm depths had increased from 19 to 34% under RT relative to CT management (P < 0.05). Crop residue additions also significantly increased MWD by 22% at the top 5 cm (P < 0.01) compared to treatments without residue in oxidic Ferralsols. At all the three sites, tillage resulted in greatest shifts of bacterial and fungal community composition, while cropping system had largest positive effect on the total microbial diversity indices. Total microbial diversity indices as well as MWD were higher in soybean-maize intercropping systems than under rotation or continuous maize cropping. Changes in total bacterial diversity related inversely to changes in the amount of free silt + clay, while fungal diversity related inversely to the contents of soil macro-aggregates >2 mm (P < 0.05). We conclude that RT plus supply of organic resources and intercropping are best strategies to increase total diversity of soil bacteria and fungi and