Despite the social and economic importance of swine farming, this activity has great polluting potential due to the large wastewater generation composed of high micropollutant concentrations, such as trace metals (Zn and Cu). Microalgae can integrate the solutions to overcome these challenges by obtaining value-added biomass, closing the loop for an environmentally and economically sustainable wastewater treatment technology. Therefore, this study aimed to identify the interference of different Zn concentrations (0.5 to 70 mg/L) in SW on the performance of high-rate algal ponds considering real treatment and biodegradation conditions via microalgae. The innovative results showed that N-NH₄⁺ removal was compromised with high Zn concentrations due to nitrification inhibition. Oppositely, the removal of soluble P was enhanced under conditions that favored algal growth (40 and 55 mg Zn/L). Moreover, Zn conferred an increase in soluble chemical oxygen demand that changed from 190 mg/L at the beginning of the treatment to 624 mg/L at the end due to extracellular polymeric substances production. Sequential chemical extraction demonstrated that biomass growth had an important contribution to Zn removal; however, it did not exceed the contribution of carbonates (28.7–44.2 %). The biomass characterization showed that Zn did not significantly affect the levels of proteins (41.2–53.5 %) and carbohydrates (34.0–43.5 %), while the lipids content was higher (18.2 %) in 55 mg Zn/L. The effects of Zn on nutrient removal and the biomass's biochemical composition must be pondered to combine the recovery of metals and nutrients and the production of value-added biomass.