Scalable lab-scale photobioreactors are needed for the exploration of new and improved photoautotrophic bioprocesses. Microbioreactor systems in which parallel bioreactors operate automatically are frequently employed to increase the speed of strain selection as well as the bioprocess-based exploration of heterotrophic fermentation processes. To enable the photoautotrophic operation of a commercially available parallel microbioreactor system with 48 stirred-tank bioreactors, LED illumination modules were designed to allow for individual light supply (400–700 nm) for each of the parallel bioreactors automated by a liquid handling station that performs both individual pH control and OD750 detection. The illumination modules enable dynamic variation of the incident light intensities of up to 1800 µmol m−2 s−1. Automated liquid level detection and volume control of each individual mL-scale gassed photobioreactor has to be established to compensate for evaporation because of the long process times of several days up to weeks. Photoautotrophic batch processes with Microchloropsis salina that employ either varying constant incident light intensities or day and night dynamics resulted in a standard deviation of OD750 of up to a maximum of 10%, with the exception of high-photoinhibiting incident light intensities. The established photoautotrophic microbioreactor system enables the automated investigation of microalgae processes in up to 48 parallel stirred photobioreactors and is thus a new tool that enables efficient characterization and development of photoautotrophic processes with microalgae.