Anaerobic digestion of animal manure generates biogas and removes biodegradable organic matter, while most of the nitrogen and phosphorous remains at very high levels after the process. A subsequent microalgae culture in the digestate provides nutrient uptake at very low operational and installation costs. However, the dark color of manure digestate prevents light penetration, reducing the rates of algae growth. Ozonation was researched as a strategy for color removal followed by microalgae culture. Although similar biomass production was achieved in treated and untreated digestates (1.09 vs. 0.99 g L−1), the positive effect of ozonation was evidenced by the significantly higher rates of photosynthetically produced oxygen: 0.804 and 0.18 mg O2 mg−1 TSS min−1, respectively, in ozonated and untreated digestates, revealing a four times higher rate of algae activity. However, this considerable higher activity was not correlated with better performance in nutrient removal since the microalgae treatment was assayed at a considerably reduced scale with a high ratio of illumination per volume. An operational costs analysis revealed that ozonation could be competitive against other strategies of color reduction such as dilution or coagulation/flocculation processes.