Emerging organic pollutants s have always been the greatest environmental concern due to their ubiquity and distinguished adverse effects. These are mostly water-bone pollutants flagged as endocrine disruptors and can greatly inconvenience the ecosystem. Among others, β-blockers have also been detected in the environment at various concentrations that threaten the well-being of humans and animals. In this work, NH2-MIL-101(Cr) doped magnetic nanoparticles nanocomposite was successfully synthesised and characterised using analytical techniques such as X-ray diffraction spectroscopy (XRD), scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), Brunauer-Emmett-Teller (BET) and transmission electron microscopy (TEM). The Fe3O4@NH2-MIL-101(Cr) was then used as an adsorbent to extract the selected β-blockers in the environmental wastewater. The selected β-blockers were quantified using a high-performance liquid chromatography-diode array detector (HPLC-DAD). Parameters affecting the extraction were screened and optimised using fractional factorial design (FFD) and central composite design (CCD), respectively. Under optimum conditions, the LODs were 0.057 and 0.065 µg L− 1, and LOQs were 0.19 and 0.22 µg L− 1 for acebutolol (ACE) and metoprolol (MET), respectively. The calibration curve exhibited the linearity range of 0.2–1200 µg L− 1 with correlation coefficients of 0.9987 and 0.9968 for ACE and MET, respectively. Repeatability studies demonstrated the %RSD of 0.63 and 0.74% for MET and ACE. At the same time, reproducibility studies displayed the %RSD of 1.057 and 1.178% for MET and ACE, respectively. Spike recovery experiments were carried out to assess the performance of MSPE in real samples, and over 88% of both analytes were recovered. This indicated that the MSPE method could enrich various organic pollutants from different environmental matrices.