An atmospheric pressure chemical ionization source has been used to enhance the potential of gas chromatography coupled with quadrupole time-of-flight (QTOF) mass spectrometry (MS) for screening and quantification purposes in pesticide residue analysis. A screening method developed in our laboratory for around 130 pesticides has been applied to fruit and vegetable samples, including strawberries, oranges, apples, carrots, lettuces, courgettes, red peppers, and tomatoes. Samples were analyzed together with quality control samples (at 0.05 mg/kg) for each matrix and for matrix-matched calibration standards. The screening strategy consisted in first rapid searching and detection, and then a refined identification step using the QTOF capabilities (MS(E) and accurate mass). Identification was based on the presence of one characteristic m/z ion (Q) obtained with the low collision energy function and at least one fragment ion (q) obtained with the high collision energy function, both with mass errors of less than 5 ppm, and an ion intensity ratio (q/Q) within the tolerances permitted. Following this strategy, 15 of 130 pesticides were identified in the samples. Afterwards, the quantitation capabilities were tested by performing a quantitative validation for those pesticides detected in the samples. To this aim, five matrices were selected (orange, apple, tomato, lettuce, and carrot) and spiked at two concentrations (0.01 and 0.1 mg/kg), and quantification was done using matrix-matched calibration standards (relative responses versus triphenyl phosphate used as an internal standard). Acceptable average recoveries and relative standard deviations were obtained for many but not all pesticide-matrix combinations. These figures allowed us to perform a retrospective quantification of positives found in the screening without the need for additional analysis. Taking advantage of the accurate-mass full-spectrum data provided by QTOF MS, we searched for a higher number of compounds (up to 416 pesticides) in a second stage by performing extra data processing without any new sample injection. Several more pesticides were detected, confirmed, and/or tentatively identified when the reference standard was unavailable, illustrating in this way the potential of gas chromatography-QTOF MS to detect pesticides in addition to the ones targeted in quantitative analysis of pesticides in food matrices.