A solid-phase extraction (SPE) method using three-dimensional covalent organic framework (COFs) coupled with ultra-high performance liquid chromatography-mass spectrometry was developed for the detection of 13 fluoroquinolones (FQs) in bean sprout samples. Critical extraction parameters influencing SPE efficiency were optimized and matrix-matched standard curves were used to eliminate matrix effects and validate the proposed method. The analytical method proved to have good linearity in the concentration range of 1.0–100 μg L–1 with correlation coefficients of r≥0.9995. The limits of detection were 0.10–0.45 μg kg–1, whereas the limits of quantification were 0.34–1.51 μg kg–1. The recoveries ranged from 92.7 % to 105 % with satisfactory precision (< 4.82 %). The COFs-packed SPE cartridge maintained recovery efficiency for the target FQs over five reuse cycles. The adsorption selectivity was mainly attributed to π–π interactions, hydrogen bonding, and electrostatic attraction between FQs and the adsorbent. Analysis of actual samples revealed the presence of enrofloxacin, ciprofloxacin, and norfloxacin in three batches of bean sprout samples. These results highlight the importance of monitoring antibiotics residues in bean sprouts.