The evolving effects of climate change and intensive agricultural practices have adversely affected soil health and crop yields. This necessitates the need to maintain and improve soil health for sustainable food production. Biochar, a carbon-rich material produced from pyrolysis of biomass is being considered as a novel soil amendment that can potentially restore soil health and improve crop yields. Several studies have reported both positive and negative effects of biochar on crop yields while focusing mainly on one type of biochar and a single plant cultivar. However, the effects of different types of biochar and its interaction with plants with different genetic backgrounds has remained unexplored. In this study, we evaluated the impact of six different biochars on the growth performance and fruit quality of three tomato (Solanum lycopersicum) cultivars. The hypotheses that (1) biochars derived from different feedstock sources would produce unique phenotypes in a single cultivar of tomato, and (2) single feedstock-derived biochar would produce different phenotypes in each of the three tomato cultivars were supported by obtained results. This study demonstrated that plant genetic background and biomass source are important variables to consider for using biochar as a soil amendment.