Biochar amendments are widely recognized to improve crop productivity and soil biogeochemical quality, however, their effects on vegetable crops are less studied. This pot study investigated the effects of cotton stick, corncob and rice straw biochars alone and with farmyard manure (FYM) on tomato growth, soil physico–chemical and biological characteristics, soil organic carbon (SOC) content and amount of soil nutrients under recommended mineral fertilizer conditions in a nutrient-depleted alkaline soil. Biochars were applied at 0, 1.5 and 3% (w/w, basis) rates and FYM was added at 0 and 30 t ha−1 rates. Biochars were developed at 450 °C pyrolysis temperature and varied in total organic C, nitrogen (N), phosphorus (P) and potassium (K) contents. The results showed that biochars, their amounts and FYM significantly improved tomato growth which varied strongly among the biochar types, amounts and FYM. With FYM, the addition of 3% corncob biochar resulted in the highest total chlorophyll contents (9.55 ug g−1), shoot (76.1 cm) and root lengths (44.7 cm), and biomass production. Biochars with and without FYM significantly increased soil pH, electrical conductivity (EC) and cation exchange capacity (CEC). The soil basal respiration increased with biochar for all biochars but not consistently after FYM addition. The water-extractable organic C (WEOC) and soil organic C (SOC) contents increased significantly with biochar amount and FYM, with the highest SOC found in the soil that received 3% corncob biochar with FYM. Microbial biomass C (MBC), N (MBN) and P (MBP) were the highest in corncob biochar treated soils followed by cotton stick and rice straw biochars. The addition of 3% biochars along with FYM also showed significant positive effects on soil mineral N, P and K contents. The addition of 3% corncob biochar with and without FYM always resulted in higher soil N, P and K contents at the 3% rate. The results further revealed that the positive effects of biochars on above-ground plant responses were primarily due to the improvements in below-ground soil properties, nutrients’ availability and SOC; however, these effects varied strongly between biochar types. Our study concludes that various biochars can enhance tomato production, soil biochemical quality and SOC in nutrient poor soil under greenhouse conditions. However, we emphasize that these findings need further investigations using long-term studies before adopting biochar for sustainable vegetable production systems.