Organic farming is rapidly expanding worldwide. Crop growth in organic systems greatly depends on the functions performed by soil microbes, and nutrient supply weed suppression by green manure crops input. Four red-pepper production systems were compared: 1) bare ground (conventional system); 2) hairy vetch monoculture; 3) rye monoculture; and 4) hairy vetch-rye mixture. Soil inorganic N reached the peak at 30 DAI and hairy vetch monoculture was the highest ($192mg;kg^{-1}$) and soil total carbon was fluctuated sporadically during the experiment. Carbohydrate and phenolic compounds in soil kept significantly higher in green manure crops systems from 10 DBI to 30 DAI, however the level was the maximum at 10 DBI (carbohydrate) and 30 DAI (phenolic comounds). Incorporation of green manure crops residue enhanced soil microbial biomass C and N throughout the growing season except that MBN in rye was reduced after incorporation. Green manure crops systems suppressed weed occurrence and, in particular, it was prominent in rye monoculture. Mineral elements composition and production in red-pepper fruits were markedly decreased in green manure crops systems although hairy vetch monoculture has come close to bare ground (NPK-applied). Therefore, it was suggested that higher biomass production should be performed not only to improve soil quality and suppress weeds but to yield suitable red-pepper fruits in green manure crops-based organic farming.