Anaerobic digester effluent containing high levels of ammonia poses a threat to the environment. To hinder this issue, a modern and promising treatment method incorporates both microalgae and their bioconversion potential. When culturing Chlorella vulgaris at a 1:7 digestate supernatant dilution ratio, biomass concentration was 1.33 g L−1 and 66% of ammonia nitrogen was removed. Furthermore, a prior nitrogen-starved seed method, namely over-compensation strategy, was applied to improve both biomass production and nutrient removal. By using nitrogen-starved seeds after a 48 h nitrogen-free stimulation, biomass yield increased by 1.7-times to 2.56 g L−1. Simultaneously, ammonia nitrogen and total phosphorus removal efficiencies reached 99% and 97% respectively. The enhanced production corresponds to higher chlorophyll fluorescence in the middle and late stages of the culture. In addition, the bioproduct contained 39% carbohydrates, and the proportion of polyunsaturated fatty acids in lipids was 66%. These findings demonstrated that the over-compensation strategy contributed to greater nitrogen removal and high-value bioproduct production in the microalgae-digestate treatment system.