High rate algal ponds (HRAPs) can efficiently treat digestates but large area footprints limit their wider application. Deep HRAPs combining sunlight with light-emitting diodes (LEDs) can reduce area requirements if enough light is supplied for microalgae photoaeration. In this work, microalgae and bacterial communities were characterized in-depth to assess the feasibility of a LED-enhanced deep HRAP (h= 1.2 m, 1.25 m3) to efficiently treat digestate at concentrations of 5%, 25% and 50% (v/v). The LEDs effects were evaluated by comparisons with a conventional HRAP (h= 0.3 m), with the same working volume but 75% more area, operated in parallel. The LED-enhanced HRAP achieved similar or superior COD (74–76%) and TKN (66–67%) removals during operation at 5%-digestate, when supporting high cell densities (>5.0 log cell·L−1) of similar communities of photosynthetic chlorophytes, such as Chlorella sp. and Dictyosphaerium sp. Despite achieving lower removals at 25% and mainly at 50%-digestate, due to limited light availability for microalgae photoaeration, LEDs supported a more mixotrophic community along with higher chlorophyll and carotenoids content in the cells. For both HRAPs, chlorophyll-a:carotenoids ratios above 1 were concomitant to high photoaeration, achieved in the LED-enhanced HRAP when at least 0.015 mol·g TSS−1·d−1 were supplied in the aphotic zone. Similar bacterial communities dominated both HRAPs, with Burkholderiaceae and Verrucromicrobia indicating high photoaeration. Nitrosomonadaceae, Nitrincolaceae and Denitratisoma were likely the main responsible for nitrogen removal. Combining red LEDs and sunlight in deep HRAPs has a high potential for digestate treatment when extensive areas are prohibitive.