Zero-tannin (ZT) lentils have been bred for alterations in the phenylpropanoid pathway to reduce tannins from their seed coats. The reduction of seed tannins can alter the chemical composition of roots and rhizodeposits, with unknown consequences for rhizosphere carbon (C) cycling and soil organic matter formation as a result of changes in substrate quality for soil microorganisms. We characterized soil microbial community structure and quantified the fate and distribution of root derived C in rhizosphere soils of ZT and conventional tannin containing genotypes using 13C isotope labelling and phospholipid fatty acid (PLFA) 13C stable isotope probing. We hypothesized that (i) rhizosphere microorganisms would assimilate more root-derived C from ZT vs. conventional tannin (TAN) lentil genotypes due to lower phenolic content, and (ii) the structure of the microbial community would be differentiated between ZT and TAN genotypes, whereby r- and K-strategists would dominate consumption of ZT and TAN rhizodeposits, respectively. Total PLFA and 13C incorporation into PLFAs was consistently higher in TAN than ZT soils indicating that microorganisms in TAN soils assimilated more root derived C, which may lead to a reduction in soil C retention through fewer microbial residues and by-products. Neither the percentage of C derived from rhizodeposition nor root biomass was significantly different between TAN and ZT genotypes. As such, differences in microbial community structure and 13C assimilation reflect differences in the quality (i.e., composition), not quantity, of rhizodeposits between TAN vs. ZT genotypes. Results from our study are in contrast to our hypothesis and suggest that rhizodeposition under ZT genotypes contain less readily available forms of C. Moreover, increased C cycling enzyme activity under ZT genotypes may result in increased decomposition of soil organic matter, exacerbating CO2 emissions and energy losses. Our study highlights that crop breeding for desirable aboveground targets has consequences to belowground soil microorganisms and functions.