Microalgae present promising green economy applications in the energy and biorefinery sectors. The work concerns a pilot study on the integration of anaerobic digestion with microalgae cultivation for managing at the same time emissions and digestate from the dry anaerobic treatment of organic waste. Biogas produced was used to feed Solid Oxide Fuel Cell after a filtering step for removing toxic compounds. The exhausts and digestate were used for providing carbon and nutrients for microalgae growth. The experimental workflow includes the characterization of both for defining their suitability in the microalgal growth (Chlorella vulgaris) tests. The exhausts of Solid Oxide Fuel Cells showed relatively stable concentration of CH4 (4–7%) and CO2 (93–96%) and low concentrations (sub ppm(v)) of sulphur, carbonyl and carboxyl, and aromatic compounds and terpenes, making it particularly suited for algae growing as compared with internal combustion engines. The challenging growing conditions are a compromise between carbon recovery and use of digestate. A good microalgae growth has been obtained (22.31 mm3 mL−1 of biovolume corresponding to 151 dry mg L−1 day−1) exploiting ammonia and phosphate from dilute digestate (removal efficiency 94% and 30% respectively) as well as a good carbon recovering (310 mg CO2 L−1 day−1). Based on our data, the integration of microalgae growth and anaerobic digestion process seems a viable solution to achieve (i) reduced emissions due to carbon recovery; (ii) optimum integrated management of anaerobic digestion waste and (iii) biomass production by low-cost nutrients and carbon.