In this research work the biotreatment of traditional Greek Pudding Dessert production line's wastewater (PDW-Pudding Dessert Wastewater) of a confectionery industry was studied, combining an attached growth aerobic biological filter as pretreatment step and a cyanobacteria-based cultivation system, with the aim to develop a viable treatment process providing simultaneously high-value biomass production. Initially, experiments in attached growth pilot-scale bioreactor were performed using various initial concentrations of dissolved Chemical Oxygen Demand (of about 1000, 2500, 5500, 7500 and 10,500 mg d-COD L−1) and two recirculation rates (1.0 and 0.5 L min−1), achieving d-COD and sugars removal up to about 75–92 % and 99 %, respectively. Then, the biologically pretreated effluent was further treated (without sterilization) using a cyanobacteria-based system. Three different cyanobacteria species (Leptolyngbya sp., Arthrospira sp. and Geitlerinema sp.) were examined separately, achieving significant d-COD (up to 83 %), NO3−-N (up to 95.5 %) and PO43− (up to 99.5 %) removal. Carbohydrates, proteins, chlorophyll-a and phycocyanin contents were also measured in Dry Weight (DW) (up to about 23.4 %, 40.7 %, 27.70 mg g−1 DW and 64.39 mg g−1 DW, respectively). The proposed hybrid system combines both efficiency and sustainability since can efficiently treat PDW (total d-COD, NO3−-N and PO43− removal up to about 98.9 %, 99.5 % and 99.7 %, respectively), reducing simultaneously the operational costs via the recovery of high added value compounds.