Combustion and emission characteristics of Egyptian sugarcane bagasse and cotton stalks powders were investigated in a bubbling fluidized bed combustor (BFBC) using silica sand as an inert bed material. Mixing and fluidizing characteristics of the two biomass materials and bed material of a certain size distribution were studied. It was found that, the feed rate ranged from 70 to 113 g/min and feed rate of 51 g/min for cotton stalks and sugarcane bagasse, respectively may be suitable for better combustion characteristics in the BFBC. The effect of different operating parameters on the axial temperature and gas concentration profiles (O2, CO2, CO, H2S, SO2 and NOx) was investigated. It was found that the formation of NOX during combustion doesn’t represent a problem as the nitrogen content of fuel is low, the bed temperature of fluidized bed is below 900 °C, and the particle size of the biomass is small. It was found that combustion efficiency ranged from 90 to 100% and from 93 to 98.8% for sugarcane bagasse and cotton stalks, respectively. Thermal efficiency was found to be in the range of (33.7–41%) and (32.5–48.7%) for sugarcane bagasse and cotton stalks, respectively. A verification model for mass and heat balance of combustion experiments was constructed to confirm that the measured values of different parameters were measured accurately with acceptable percent of error.