The present study outlines a process for the cost-effective production of 13 C/ 15 N-labelled biomass of microalgae on a commercial scale. The core of the process is a bubble column photobioreactor with exhaust gas recirculation by means of a low-pressure compressor. To avoid accumulation of dissolved oxygen in the culture, the exhaust gas is bubbled through a sodium sulphite solution prior to its return to the reactor. The engineered system can be used for the production of 13 C, 15 N, and 13 C– 15 N stable isotope-labelled biomass as required. To produce 13 C-labelled biomass, 13 CO 2 is injected on demand for pH control and carbon supply, whereas for 15 N-labelled biomass Na 15 NO 3 is supplied as nitrogen source at the stochiometric concentration. The reactor is operated in semicontinuous mode at different biomass concentrations, yielding a maximum mean biomass productivity of 0.3gL −1 day −1 . In order to maximize the uptake efficiency of the labelled substrates, the inorganic carbon is recovered from the supernatant by acidification/desorption processes, while the nitrate is delivered at stochiometric concentration and the harvesting of biomass is performed when the 15 NO 3 − is depleted. In these conditions, elemental analysis of both biomass and supernatant shows that 89.2% of the injected carbon is assimilated into the biomass and 6.9% remains in the supernatant. Based on elemental analysis, 97.8% of the supplied nitrogen is assimilated into the biomass and 1.3% remains in the supernatant. Stable isotope-labelling enrichment has been analysed by GC–MS results showing that the biomass is highly labelled. All the fatty acids are labelled; more than 96% of the carbon present in these fatty acids is 13 C. The engineered system was stably operated for 3 months, producing over 160g of 13 C and/or 15 N-labelled biomass. The engineered bioreactor can be applied for the labelling of various microalgae.