Within the biorefinery concept, microalgal cultivation has potential as one component of the wastewater treatment toolkit for anaerobic digestates. Recovering nutrients from digestate such as anaerobic digestate of piggery effluent, has been well demonstrated with Scenedesmus sp. and Chlorella sp. in mixed cultures. Less understood during microalgae cultivation, is the participation of bacterial communities as they play a fundamental role in biological nutrient cycling processes with potential to optimise algal productivity and nutrient recovery. To this end, we batch cultivated microalgae on increasing concentrations of digestate (250, 500 and 890 mg N NH4+ L−1), took samples under time series and quantified culture conditions including water chemistry properties with a focus on nitrogen values during treatment. Chlorophyll and dry weight were measured to provide reasonable estimates of the health of the microalgal culture. We additionally characterised the bacterial community using next generation 16S rRNA sequencing on the ION torrent, followed by an in-silico analysis of functional nitrogen and carbon cycling genes using PICRUSt. Our data suggest the microalgae form symbiotic relationships with a number of bacterial groups including Bacteriodetes, Cyanobacteria, nitrifying and N-fixing bacteria. These microalgae-microbial consortia favour NH4+ and NO2− removal possibly via nitrification and nitrifier denitrification pathways while accumulating NO3− in the inoculated diluted digestate treatment systems. In the absence of inoculation and at high ammonium concentrations in the digestate, almost all NH4+, NO2− and NO3− are driven from the system, largely due to stripping and are unable to be captured for any further use. Thus, a microalgae-microbial consortia-driven digestate treatment system offers the potential to recapture and recover N, enabling production of N fertiliser. These data demonstrate the integral role of syntrophic relationships for microalgae and bacteria in third generation biorefinery concepts.