Intentional amendment of soil with charcoal (called biochar) is a promising new approach to sequester atmospheric carbon dioxide and increase soil fertility. However, the environmental properties of biochars can vary with production conditions, making it challenging to engineer biochars that are simultaneously optimized for carbon sequestration, nutrient storage, and water-holding capacity. We report here the systematic characterization of biochars produced under a variety of highly controlled pyrolysis conditions from two biomass feedstocks (corn stover and apple wood). Our results suggest that the chemical composition and physical structure of biochars are determined not just by the maximum heat treatment temperature, but also by several other factors that include the pyrolysis heating rate, treatment time at the maximum temperature and particle size. We also test a new approach that combines reactivity measurements, diffusion-reaction theory and structural models to overcome some of the challenges encountered in characterizing the complicated pore structure of biochars.