BACKGROUND The presence of pharmaceutical compounds has been studied in several countries in Latin America, and many xenobiotic compounds have been identified in wastewater, surface water and even drinking water, including ibuprofen and diclofenac. Microalgal‐based systems have been identified as a good alternative for removing these micropollutants, particularly under tropical conditions, and they are associated with low operational cost and high removal efficiency. Although studies for removing pharmaceutical compounds with Parachlorella kessleri are scarce, this microalga has demonstrated good performance in the treatment of wastewater. RESULTS Using doses of ibuprofen of 1000 and 16 000 μg L−1 and of diclofenac of 100 and 500 μg L−1, the removal efficiency of P. kessleri was evaluated under controlled conditions for periods of 12, 48 and 96 h during cell growth. A hormesis process was identified after an alarm phase at the first 12 h and a recovery at 48 h for ibuprofen, because the diclofenac curve achieved an early death phase, which was associated with oxidative damage. Total removal of up to 51.3% and 55.7% was obtained for ibuprofen and diclofenac, respectively. These removal efficiencies were mostly influenced by microalgae by the process of bioaccumulation/adsorption (23.3% for ibuprofen and 37.1% for diclofenac) and by other mechanisms (40.6% for ibuprofen and 44% for diclofenac). CONCLUSION Removal efficiencies were mainly associated with the presence of microalgae and removal mechanisms such as bioaccumulation and biodegradation for diclofenac, and biodegradation for ibuprofen. © 2021 Society of Chemical Industry (SCI).