BACKGROUND Whereas multi‐species biofilm reactors are commonly used for the treatment of liquid and solid wastes, new strategies are progressing for the development of single species biofilm for the production of high‐value metabolites. Technically, this new concept relies on the design of bioreactors able to promote biofilm formation and on the identification of the key physico‐chemical parameters involved in biofilm formation. RESULTS An experimental setting comprising a liquid continuously recirculated on a metal structured packing has been used to promote Bacillus subtilis GA1 biofilm formation. The colonization of the packing has been visualized non‐invasively by X‐ray tomography. This analysis revealed an uneven, conical, distribution of the biofilm inside the packing. Compared with a submerged culture carried out in a stirred tank reactor, significant modification of the lipopeptide profile has been observed in the biofilm reactor with the disappearance of fengycin and iturin fractions and an increase of the surfactin fraction. In addition, considering the biofilm reactor design, no foam formation has been observed during the culture. CONCLUSIONS The configuration of this biofilm reactor set‐up allows for a higher surfactin production by comparison with a submerged culture while avoiding foam formation. Additionally, scale‐up could easily be performed by increasing the number of packing elements. © 2013 Society of Chemical Industry