In this study, a recombinant non-pathogenic Pseudomonas putida KT2440 was applied for rhamnolipid or 3-(3-hydroxyalkanoyloxy)alkanoic acid production. The production and recovery of these surfactants was intensified by the integration of foam fractionation and desorption techniques into the bioreactor cultivation process. Furthermore, the accumulation of bacteria at the gas-liquid interface of the foam could be diminished by deleting genes encoding hydrophobic cell-surface structures.