Biodegradation of an actual petroleum wastewater sample collected from an oil refinery site in Guwahati, India has been carried out in a packed bed reactor (PBR) by Bacillus cereus (AKG1 MTCC9817 and AKG2 MTCC9818) strains immobilized in the calcium−alginate beads. The biodegradation of petroleum wastewater has also been performed by biofilm of the isolated B. cereus strains grown on the polyurethane foam (PUF). The performances of both the systems have been evaluated by measuring the chemical oxygen demand (COD), total organic carbon (TOC), concentration of phenolic compounds, total phosphate-phosphorus (PO43−−P) and ammonium−nitrogen (NH4+–N) levels in the wastewater during the microbial treatment. The initial COD of 9200mg/L, TOC of 4548mg/L, phenolics of 3561mg/L, PO43—P of 121.1mg/L and NH4+–N of 121.09mg/L were reduced to 70mg/L, 184.97mg/L, 8mg/L, 67.3mg/L and 61.3mg/L, respectively as a result of biodegradation in the PBR with alginate beads. On the other hand, treatment in the PUF-based PBR led to a final COD, TOC, phenolics, PO43—P and NH4+–N level of 830mg/L, 545.64mg/L, 303mg/L, 89.8mg/L and 69.3mg/L, respectively. Overall, present results demonstrated the successful implication of immobilized AKG1 and AKG2 in treating petroleum wastewater in the PBRs.