The anaerobic digestion effluent (ADE) generated from biogas projects has raised increasing environmental concerns. In this study, the algal cells integrity, pollutants degradation and the community compositions shifts were evaluated during the ADE treatment with simultaneous biodiesel accumulation in photobioreactors (PBR). The operation of six PBRs was initiated with diluted ADE (625, 393, 272, 193, 178 and 167 mg/L SCOD). The results showed that the high concentration of ADE (625 mg/L SCOD) led to considerable inhibition of algal cells growth. By comparison, the PBR (272 mg/L SCOD) attained the maximum lipid productivity (59.13 mg/L.d), and complete nutrient (nitrogen and phosphorus) removal was observed in PBR (167 mg/L SCOD). Moreover, the highest viable algal cells (86.2%) was attained in PBR (272 mg/L SCOD). Therefore, this study provides a feasible technology for microalgal cultivation with simultaneous treatment of ADE in PBRs. In addition, the approach of excitation-emission matrices with parallel factor (EEMs-PARAFAC) was utilized to further understand the organics degradation. The removals of component 1 (humic-like) and component 2 (protein-like, biological production) were ascended by the increased algal and bacteria activity in the microalgal-bacterial consortium. Additionally, the community composition analysis illustrated that bacterial diversity was reduced by the inoculation with microalgae, which was attributed to the formation of stable function groups with satisfactory contaminant degradation abilities and good algal cell growth; and Chlorella species were dominant, which benefited biodiesel accumulation in PBRs. These findings demonstrated the potential of using a bacterial-microalgal consortium for ADE purification simultaneous biodiesel production.