A closed atmospheric pressure chemical ionization (APCI) ion source as interface between a gas chromatograph (GC) and a triple quadrupole mass spectrometer (QqQ-MS) was developed. The influence of different ion source conditions, such as humidity, make-up gas flow, and the position of the GC column, were investigated and determined as main factors to increase sensitivity and repeatability of the system. For a performance test under real conditions, the new APCI ion source was used for the determination of plant protection products in commercially available coffee beans from Vietnam. The ionization behavior was investigated and the majority of the analytes were detected as [MH]+, [M]+∙, or as characteristic fragment ions, which have been assigned to ion source fragmentation. The developed GC-MS methods are based on tandem MS (MS/MS) and revealed for the plant protection products limits of detection (LOD) between 1 and 250 pg on column and relative standard derivations for all compounds < 16%. The used ultrasonic solid-liquid extraction yielded recovery rates of approximately 60 to 100%. Residues of herbicide methyl esters, organophosphorus compounds, and organonitrogen compounds have been detected in the analyzed coffee beans.