We studied long-term (64.5 weeks) biodegradation of diesel fuel, diesel/biodiesel blends (B10-B90) and biodiesel fuels in urban soil microcosms containing indigenous microorganisms, or indigenous microorganisms augmented with a hydrocarbon-degrading bacterial community. Mineralization extent (mmol of CO2 per day) of B10-B30 blends was smaller compared with diesel fuel at both short- (28 days) and long-term (109 days), and increased with biodiesel content. Priming with hydrocarbon degraders accelerated mineralization in the short-term (by up to 140%), with highest influence using blends with lower biodiesel content, but did not significantly influence kinetics and mineralization extent in the long-term. Although the biodiesel fraction was degraded completely within 64.5 weeks, 3–12% of the total aromatic and aliphatic hydrocarbons remained in the microcosms. Barcoded 16S rRNA gene MiSeq sequencing analysis revealed a significant effect of blend type on the community structure, with a marked enrichment of Sphingobacteriia and Actinobacteria classes. However, no significant influence was determined in the long-term, suggesting that the inoculated bacterial community may not have survived. Our findings show that biodiesel is preferentially degraded in urban soil and suggest that the value of bioaugmentation for bioremediating biodiesel fuels with hydrocarbon-degrading bacteria is limited to short-term exposures to lower (B10-B30) blends.