Anaerobic digestion of food wastes coupled with digestate post-treatment using microalgae-based systems could recover large amounts of energy and nutrients worldwide. However, the development of full-scale implementations requires overcoming microalgae inhibition by high ammonia concentrations and low light transmittances affecting photosynthesis. This study evaluated the potential of microalgae-based reactors supplied with red light-emitting diodes (LEDs) at low intensity (660 nm and 15 µmol·m−2·s−1) to treat food waste digestate. LED reactors were compared with control reactors exposed to solar radiation. From a range of species in the inoculum, Chlorella vulgaris showed high adaptation to both lighting regimes and digestate environmental conditions, characterized by a C:N:P ratio of 74:74:1. Removal efficiencies for control and LED reactors were 84.0% and 95.8% for soluble chemical oxygen demand (COD) and 89.4% and 53.0% for ammonia, respectively. Approximately 50% of ammonia in control reactor and 15% in LED reactor was lost from the systems, whereas 17% and 36% of ammonia was transformed to organic nitrogen in control and LED reactors, respectively. Low-intensity LEDs maintained microalgae growth in levels similar to solar radiation and supported efficient digestate treatment, showing a potential for further application in optimization of full scale reactors at a relatively low energy cost.