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This study presents a novel approach for optimizing GC-MS/MS performance and ensuring the reproducibility of pesticide residue analysis across diverse food matrices. Analysis of thermally treated (100–280 °C) extracts using GC-MS (scan mode) and FTIR revealed that strawberry and dry mint contain significantly higher concentrations of non-volatile co-extractives of varying chemical natures compared to fennel seeds. It was further elucidated that polar non-volatile co-extractives exhibit a more pronounced negative impact on analytical performance. Consequently, a synergistic approach was developed for strawberry analysis, combining end-column back-flushing with the application of fennel extract as a Natural Analyte Protectant (NAP). For dry mint, optimal results were achieved through a different approach: standard forward carrier gas cleaning combined with a fivefold sample dilution. The developed protocols enabled the efficient analysis of 195 pesticides in strawberries, all achieving LOQs of 0.01 mg/kg. Results demonstrated high precision (RSD < 3% for most analytes) and excellent recoveries (90–110%) at 0.01 and 0.05 mg/kg. Furthermore, 154 and 186 pesticides were successfully validated in dry mint with LOQs of 0.01 and 0.05 mg/kg, respectively. This research demonstrates that efficient column cleaning can be achieved through either back-flushing or the same forward-flow of the carrier gas, depending on whether the non-volatile co-extractives are polar or non-polar. Finally, ethyl acetate (EtOAc) fennel extract is introduced as a highly effective NAP, which is especially advantageous for samples lacking endogenous volatile components while simultaneously containing high concentrations of polar co-extractives. Pesticide residue monitoring was applied for 20 commercial samples, demonstrating high sensitivity. While strawberry samples exhibited excellent regulatory compliance and a total absence of chlorpyrifos, herbal matrices showed a higher chemical burden characterized by multi-residue co-occurrence and MRL exceedances.