Third generation biofuels, e.g. biofuels production from algal biomass, have gained attention due to increased interest on global renewable energy. However, crop-based biofuels compete with food production and should be avoided. Microalgal cultivation for biofuel production offers an alternative to crops and can become economically viable when combined with the use of used water resources. Besides nutrients and water, harvesting microalgal biomass represents one of the major costs related to biofuel production and thus efficient and cheap solutions are needed. In bacterial-algal systems, there is the potential to produce energy by co-digesting the two types of biomass. We present an innovative approach to recover microalgal biomass via a two-step flocculation using bacterial biomass after the destabilisation of microalgae with conventional cationic polymer. A short solids retention time (SRT) enhanced biological phosphorus removal (EBPR) system was combined with microalgal cultivation. Two different bacterial biomass removal strategies were assessed whereby bacterial biomass was collected from the solid-liquid separation after the anaerobic phase and after the aerobic phase. Microalgal recovery was tested by jar tests where three different chemical coagulants in coagulation-flocculation tests (AlCl3, PDADMAC and Greenfloc 120) were assessed. Furthermore, jar tests were conducted to assess the microalgal biomass recovery by a two-step flocculation method, involving chemical coagulants in the first step and bacterial biomass used in the second step to enhance the flocculation. Up to 97% of the microalgal biomass was recovered using 16 mg polymer/g algae and 0.1 g algae/g bacterial biomass. Moreover, the energy recovery by the short-SRT EBPR system combined with microalgal cultivation was assessed via biomethane potential tests. Up to 560 ± 24 mL CH4/gVS methane yield was obtained by co-digesting bacterial biomass collected after the anaerobic phase and microalgal biomass. The energy recovery in terms of methane production obtained in the short-SRT EBPR system is about 40% of the influent chemical energy.