Photobioreactors are a promising alternative for piggery wastewater treatment which allows to produce valuable biomass, but the presence of antibiotics or heavy metals in the pig manure can influence the biomass composition and the posterior valorization processes. This study evaluates the effect of these pollutants on mass, composition and hydrolysis yields of the consortia of microalgae and bacteria obtained in a 1280 L photobioreactor treating pig manure. The photobioreactor feed was doped with 1) veterinary antibiotics; 2) copper, zinc, and arsenic; and 3) combination of both pollutants. The pollutants presence decreased the mass of biomass grown in the photobioreactor by up to 35% while glucose content of the biomass by up to 42% and increased protein and xylose by 30% and 16% due to oxidative stress. Likewise, they increased the protein solubilization yield by acid hydrolysis at 120 ºC by 32% while reduced glucose solubilization by 49% after alkaline hydrolysis at 120 ºC. Applying enzymatic hydrolysis and ultrasound assisted enzymatic extractions, glucose and xylose recoveries were drastically reduced in presence of heavy metals (∼100%). Antibiotics increased xylose solubilization by ultrasonication (74%), but also its degradation, decreasing xylose recovery. Thus, the presence of all these pollutants in pig manure affected biomass production and valorization and these results must be considered for biorefinery processes.