Microalgae biotechnology is a promising tool for many applications, including the elimination of nutrients and other contaminants from wastewater. In this work, we measured the removal efficiency of two wastewater treatment processes: an activated-sludge based conventional process and another based on microalgae biotechnology using high-rate algae ponds (HRAPs). The latter was tested using two different configurations. In the first one, HRAPs were placed after an UASB reactor and used as a tertiary treatment to remove nutrients. In the second, the UASB reactor was disconnected so the HRAPs were directly fed with pretreated wastewater. Additional treatment was performed using dissolved air flotation (DAF). The performances of both configurations (UASB-HRAP and HRAP-DAF) were compared to that of the conventional line including primary and secondary biological treatments and operating in parallel within the same wastewater treatment plant (WWTP). Sixty-four out of 81 target PhACs were detected in the influent of the WWTP, at an average concentration of 223 μg L−1, whereas 55 and 54 were measured in the conventional (14 μg L−1) and non-conventional (17 μg L−1) effluents. Average removal efficiencies were similar (94 vs. 92%) for both treatment lines when comparing total PhACs concentrations. The compositional patterns of the resulting effluents, however, were not, suggesting the occurrence of differential removal mechanisms depending on the chemicals and wastewater treatments considered. Highly consumed compounds such as ibuprofen and acetaminophen were predominant in the non-conventional effluent (>1 μg L−1), denoting lower removal than in the conventional line. On the other hand, elimination of diclofenac and some specific antibiotics and diuretics (e.g., hydrochlorothiazide) was between 15 and 50% higher using HRAPs. Overall, the efficiency of the microalgae technology removing PhACs was found to be comparable to that used in conventional WWTPs. This, combined with a higher efficiency removing nutrients, shows the potential of HRAP technology for wastewater treatment as an alternative (or addition as tertiary treatment) to more conventional approaches based on activated sludge.