Plant and animal agriculture is a part of a larger system where the environment, soil, water, and nutrient management interact. Biochar (a pyrolyzed biomass) has been shown to affect the single components of this complex system positively. Biochar is a soil amendment, which has been documented for its benefits as a soil enhancer particularly to increase soil carbon, improve soil fertility, and better nutrient retention. These effects have been documented in the literature. Still, there is a need for a broader examination of these single components and effects that aims at the complementarity and synergy attainable with biochar and the animal and crop-production system. Thus, we report a comprehensive dataset documenting the interactions of biochar with manure, soil, and plants. We evaluated three biochars mixed with manure alongside both manure and soil controls for improvement in soil quality, reduction in nutrient movement, and increase in plant nutrient availability. We explain the experiments and the dataset that contains the physicochemical properties of each biochar–manure mixture, the physicochemical properties of soil amended with each biochar–manure mixture, and the biomass and nutrient information of plants grown in biochar–manure mixture-amended soil. This dataset is useful for continued research examining both the short- and long-term effects of biochar–manure mixtures on both plant and soil systems. In addition, these data will be beneficial to extend the findings to field settings for practical and realized gains.