The effects of long-term organic residue additions on the active pool of soil organic matter, microbial biomass C and N, water-soluble C and total C and N were studied in an annual corn (Zea mays L. cv. Tuxpeno C-7)-bean (Phaseolus vulgaris L. cv. Turrialba) rotation in the humid tropics of Costa Rica. The rotation was conducted within four, 9 yr old, cropping systems: two alley cropping systems, involving leguminous trees [Erythrina poeppigiana (Walpers) O. F. Cook and Gliricidia sepium (Jacq.) Steud.], and two cropping systems without trees, either fertilized or not with N. Higher total C and N, microbial C and N, water-soluble C and soil moisture were found in the alley cropping treatments than in the treatments without trees. As compared to other tropical ecosystems total C and N values were high (40-45 and 2.4-2.8 g kg-1, respectively), but microbial biomass C and N values (without conversion factors) were relatively low (50-62 and 7-11 mg kg-1, respectively), probably due to the volcanic nature of the soils. Water-soluble C values were high, ranging from 200 to 284 mg kg-1. Seasonal changes of microbial biomass appeared to depend more on crop phenology, management practices (pesticides and fertilizer applications) and soil moisture than on pruning additions. During the year microbial C:N ratios varied from 4.5 to 5.5 in the wet period (corn crop) to 13.5-16.5 in the dry period (bean crop). Apparently, interaction among crop stovers and tree prunings results in a system which oscillates between N immobilization and mineralization.