Biodiesel industrial effluent rich in crude glycerol (CG) was processed to produce value-added product. Under continuous culture system, Bacillus amyloliquefaciens strain CD16 immobilized within its biofilm, produced 3.2 L H-2/day/L feed, over a period of 60 days at a hydraulic retention time of 2 days. The effective H-2 yield by B. amyloliquefaciens strain CD16 was 165 L/L CG. This H-2 yield was 1.18-fold higher than that observed with non-biofilm forming Bacillus thuringiensis strain EGU45. Bioprocessing of the effluent released after this stage, by recycling it up to 25% did not have any adverse effect on H-2 production by strain EGU45; however, a 25% reduction in yield was recorded with strain CD16. Biofilm forming H-2 producers thus proved effective as self-immobilizing system leading to enhanced process efficiency.