An innovative method for directly screening pesticide residues in foodstuffs was developed using ambient microfabricated glow discharge plasma (MFGDP) desorption/ionization mass spectrometry. The capability of qualitative and quantitative analysis with MFGDP–MS at atmospheric pressure on agrochemicals has been demonstrated. Nine multi-class compounds (ametryn, amitraz, buprofezin, dimethoate, diphenylamine, imazalil, isoproturon, malathion, parathion-ethyl) were examined in spiked solutions, in extracts of fruits and vegetables, and in unprocessed samples. In the standard solutions of the nine pesticides, the application of MFGDP-MS for the detection of organophosphorus, organochlorine and organonitrogen compounds was demonstrated. Limits of detection (LODs) at levels down to 0.13ngg−1mm−2 of the spiked extracts of tomato, green pepper, and orange (collected by “QuEChERS”) were obtained, with RSDs of 3.48–13.46%. In the direct analysis of unspiked peels and extracts of apple, celery and grapes, the residues of diphenylamine, dimethoate and malathion were successfully analyzed by tandem mass spectrometry (MS/MS). The distribution of diphenylamine in apples was obtained by scanning the various unprocessed parts of the apple piece-by-piece in depth directly. Thus, an MFGDP–MS, having a small size and operating at a low temperature, made it possible to directly and accurately screen for pesticide residues in fruits and vegetables in situ.