A sequential electrochemical oxidation (EO) and algal bubble column photobioreactor (BPBR) system was proposed to treat distillery wastewater (DWW). EO was carried out in a 2 L reactor with Ti-RuO2 anodes. Electrochemically oxidised DWW (EO-DWW) was then supplied to the microalgae Asterarcys quadricellulare. The EO operating current, treatment time and post-treatment dilution were optimised with a central composite design (CCD) with algal specific growth rate, lipid accumulation and photosynthetic quantum yield (Fv/Fm) as dependent variables. The optimal treatment conditions for the growth of A. quadricellulare were 27 A for 26 h and a post-treatment dilution of 8. Under optimal conditions, A. quadricellulare grew at a specific growth rate of 1.06 d−1 with a lipid accumulation of 12.7% and an Fv/Fm of 0.7. The optimal conditions were validated, and a 1.6 L bubble column photobioreactor was designed to treat the EO-DWW sequentially. The sequential EO-BPBR system removed 92% COD, 76% TOC and 82% TN from DWW. The algal biomass productivity was 0.96 g/L/d with a carbon sequestration of 550–700 mg/L/d and an aqueous carbon capture of 240–280 mg C/L/d. Additionally, the flue gas evolved from the EO reactor was analysed and contained 68% H2, 18% O2 and 12.5% CO2. The H2 in the flue gas can compensate for 26.5% of the energy spent for the EO process. The algal biomass produced in the sequential process can compensate for 6% of the total energy consumed for EO. Therefore, 32% of the energy spent on EO can be reclaimed by sequential EO-BPBR treatment.