A continuous-flow reactor (CSTR) and a soil slurry-sequencing batch reactor (SS-SBR) were maintained in 81 vessels for 180 days to treat a soil contaminated with diesel fuel (DF). Concentrations of Candida tropicalis, Brevibacterium casei, Flavobacterium aquatile, Pseudomonas aeruginosa, and Pseudomonas fluorescens were determined using fatty acid methyl ester (FAME) analysis. DF removal (biological and volatile) and biosurfactant concentrations were measured. The SS-SBR encouraged the growth of biosurfactant-producing species relative to the CSTR. Counts of biosurfactant-producing species (C. tropicalis, P. aeruginosa, P.fluorescens) relative to total microbial counts were 88% in the SS-SBR and 23% in the CSTR. Biosurfactants were produced in the SS-SBR to levels of nearly 70 times the critical micelle concentration (CMC) early in the cycle, but were completely degraded by the end of each cycle. No biosurfactant production was observed in the CSTR. DF biodegradation rates were over 40% greater and DF stripping was over five times lower in the SS-SBR than the CSTR. However, considerable foaming occurred in the SS-SBR. Reversing the mode of operation in the reactors on day 80 caused a complete reversal in microbial consortia and reactor performance by day 120. These results show that bioslurry reactor operation can be manipulated to control overall reactor performance.