In this study, we developed a spectrophotometry method for the analysis of 5-hydroxymethylfurfuraldehyde (HMF) in pharmaceutical formulations using citrate@Fe3O4 adsorbent. As bare magnetite (Fe3O4) has certain limitations, such as aggregation and oxidation, surface modifications are commonly used to improve its properties. We successfully coated Fe3O4 with sodium citrate to create a magnetic adsorbent for isolating HMF from samples. We confirmed the successful surface coating of Fe3O4 with citrate using Fourier Transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), Zeta potential, and scanning electron microscopy (SEM). The high adsorption capacity of citrate@Fe3O4 is due to the abundance of carboxyl and hydroxyl groups on the surface of the adsorbent, making it ideal for HMF extraction. The HMF concentration was then quantified using spectrophotometry. Citrate@Fe3O4 exhibited a high surface area and strong interaction with HMF. We analyzed the individual influential factors affecting the magnetic solid phase extraction (MSPE) setup. Validation parameters were also provided to confirm the reliability of the method. Under optimal parameters, the method exhibited excellent linearity in the range of 0.05–30.00 μg/ml with the lower limit of quantification (LLOQ) of 0.05 μg/ml. Relative standard deviations (RSD) values for precision were better than 10% and the method's trueness were better than 10%. Recoveries were found to be in the range of 85% to 106%, indicating excellent accuracy and reliability. We used this method to identify and measure HMF in six different dextrose pharmaceutical dosage forms as intravenous injectable solutions and three honey samples. •Synthesis and characterization of a citrate@Fe3O4 nanoadsorbent for selective HMF extraction.•Optimization of a magnetic solid phase extraction method for HMF.•Accurate HMF quantification in pharmaceutical formulations via spectrophotometric analysis.