Surveys of pesticide residues in fruit are important to demonstrate conformity with strict regulations of newly open markets for export of exotic fruit. Multi-residue methods are tools to ensure compliance with regulations and both the CEN and the AOAC have versions of QuEChERS that are used effectively as mainstream methods. The aim of this study was to assess their performance and pick the optimum one for this particular application using GC-MS. The use of graphitised carbon black (GCB) to improve clean-up was assessed. Optimisation of large volume injection (LVI) and implementation of concurrent back-flushing was needed in order to improve sensitivity at a low concentration levels for 33 pesticides (0.01 mg kg−1). Cleaner total ion current (TIC) profiles were obtained with the CEN method. Recoveries of most of the pesticides showed statistical differences (α = 0.05) when GCB was used in the AOAC method, unlike the CEN method. In general, GCB/no GCB use for CEN clean-up gave good, very similar results for all fruit, though some pesticides showed some adsorption on the GCB surface. The CEN general method was preferred since acceptable recoveries (> 80%) and RSD (< 20%) can be achieved for all analytes.