Carrot (Daucus carota L.) seed quality is affected by umbel position due to uneven maturation of carrot seeds produced in different umbel orders. However, keeping this in view, we tested whether seed quality could be improved with the suppression of tertiary umbels under exogenous auxin application. Using auxin-producing bacterial isolates, i.e., Bacillus sp. MN54, Enterobacter sp. MN17, Pantoea sp. MN34, and Burkholderia phytofirmans PsJN, the arrangements of carrot umbel order were evaluated in terms of quality carrot seed production. The results revealed that auxin production by plant-growth-promoting rhizobacteria showed significant differences among measured growth indices, yield, and seed quality attributes. The selected endophytic strains co-applied with auxin via foliar application improved all growth- and yield-related traits, as well as the enzymatic activities of carrots. Noticeably, MN17+L-tryptophan and MN34+L-tryptophan effectively minimized the number of tertiary umbels by increasing the number of secondary umbels. Furthermore, treating with PsJN+L-tryptophan and MN34+L-tryptophan resulted in reduced conductivity of seed leachates and malondialdehyde levels in primary, secondary, and tertiary umbel seeds. These findings collectively indicate the potential of the foliar application of PsJN+L-tryptophan and MN34+L-tryptophan to effectively alter umbel arrangement, leading to improved yield and seed quality. This study implies that carrot seed producers can consider employing specific PGPB strains, particularly MN34+L-tryptophan, to suppress tertiary umbels and achieve higher yields of high-quality carrot seeds.