Abstract This paper discusses the overall energy consumption and greenhouse gas emissions when extracting pigments and producing hydrogen from Spirogyra sp. microalga biomass. The energy evaluation from the biomass leftovers was also included in this work. The influence of the functional unit and different allocation criteria on the biorefinery assessments is also shown. The study consists of laboratory tests showing Spirogyra sp. growth, harvesting, drying, pigment extraction and fermentation by Clostridium butyricum. Electrocoagulation and solar drying were tested and compared to conventional centrifugation and electrical dewatering in terms of their energy consumption for harvesting and dewatering, respectively. To discuss the biorefinery viability, the pigments and biohydrogen (bioH2) retail costs are considered against operational costs according to electricity needs. The low yield of biochemical hydrogen and the high energy requirements for the pigment extraction were identified as main topics for further research. This research hopefully contributes to highlight the importance of energy and emission balances in order to decide on feasibility of the biorefinery.