In this research, a novel magnetic zirconium-based metal-organic framework (Fe3O4@SiO2@MIP-202, MMOF), was fabricated, fully characterized, and applied for the batch-mode solid phase extraction of trace amounts of Pd2+ ions from water and wastewater samples before its spectrophotometric detection. Pd2+ ions were desorbed from MMOF by nitric acid and were complexed by treating with KI solution to have a maximum absorbance at 410 nm. The synthesized MMOF composite showed a very large surface area (65 m2.g− 1), good magnetization (1.7 emu.g− 1) and a large pore volume (0.059 cm3.g− 1) with adsorption capacity of 194.5 mg of Pd2+ ions/g of the adsorbent. This nanosorbent boasts chemo-mechanical stability, high adsorption capacity due to its vast active sites, and facile recovery facilitated by its magnetic properties. Parameters affecting the extraction efficiency of the method were optimized as pH of the sample 7.4, volume of the sample 25 mL, 15 mg adsorbent, 1 mL of 0.1 M HNO3 eluent, with 10 and 15 min as the extraction and desorption times, respectively. The calibration curve was found to be linear across the 10.0–1500.0 µg.L− 1 range with a limit of detection of 1.05 µg.L− 1. The obtained extraction efficiency and enrichment were 98% and 245, respectively. The total analysis time was less than 30 min. This MMOF has never been used for the extraction of Pd2+ ions before.