Polypyrrole magnetic microspheres were synthesized and used to extract carbaryl, carbofuran, and methomyl before analysis by a high-performance liquid chromatography with diode array detection. Under optimal conditions, four times the preconcentration was achieved with the use of only 1.2 mL of sample. Good linearity with ranges of 3.0–7.5 × 103, 6.0–4.5 × 103, and 15–3.0 × 103 ng kg−1 and limits of detection of 1.37 ± 0.10, 4.7 ± 1.2, and 10.1 ± 5.7 ng kg−1 were obtained, respectively. Good reproducibility (RSDs < 5%) was achieved over 24 cycles of extraction and regeneration. Good accuracy (recoveries 81.6 ± 1.5%–108.3 ± 2.2%) and good precision (RSDs 0.11%–4.5%) were obtained. Carbaryl was detected in apple (2.75 ± 0.23 ng kg−1), carbofuran in tomato (11.34 ± 0.61 ng kg−1), and methomyl in watermelon (34.7 ± 1.7 ng kg−1). The relative expanded uncertainty of the measurement method was less than 14% for all three pesticides.