BACKGROUND: The rapidly increasing use of biotechnology in many industries has led to the need for novel methods for cell culture which provide an efficient way to either optimize or perform fermentation operations. In parallel, microfabrication techniques allowed the development of microfluidic chips for complex handling of fluids and cells. RESULTS: This work presents a microfluidic platform to trap non-adherent cells for the continuous production of a biomolecule of interest. The biological system chosen as a model was the yeast species Saccharomyces cerevisiae and the extracellular protein invertase. The use of the appropriate combination of the flow rate of the medium, medium dilution rate, and pH allowed effective control of the cell growth in the microfluidic bioreactor while at the same time maximizing the invertase activity per cell. The microfluidic bioreactor allowed for continuous cell culture for 32 h and its productivity both per cell (3.22x10(-8) U cell(-1)) and per consumed nutrient (3.79 U mg(-1) sucrose) was consistently higher than its macroscale batch and continuous reactor counterparts. CONCLUSION: This work demonstrated that a microfluidic bioreactor can be used for continuous production of an extracellular protein using hydrodynamically trapped non-adherent yeast cells. (C) 2016 Society of Chemical Industry