Producing defensible data for legal proceedings requires strict monitoring of sample integrity. In fire debris analysis, various approved packaging and storage solutions are designed to achieve this by preventing cross-contamination. This study examines the efficiency of current practices at preventing cross-contamination in the presence of a sample matrix (charred wood) via analysis by comprehensive multidimensional gas chromatography coupled with time-of-flight mass spectrometry (GC×GC-ToF MS). The transfer of ignitable liquid residue (ILR) was assessed by comparing percentages of the target ILR area relative to the total chromatogram area and applying chemometric tools developed to detect cross-contamination. All practices reduced cross-contamination in comparison to faulty packaging. Individual practices varied in their performance. Nylon-based packaging performed best, whereas commercial polyethylene-based packaging performed worst due to interfering compounds emitted from the material and sealing mechanism. Heat-sealing was the best sealing mechanism when applied correctly, followed by press-fit connections, and lastly, adhesive sealing. Refrigerated storage offered several advantages, with elevated impact for polyethylene-based packaging and adhesive sealing mechanisms. Triple-layer packaging practices did not show significant benefits over double-layers. The recommended packaging approach based on these findings is mixed-material packaging (metal quart can in a heat-sealed nylon bag), offering advanced prevention of cross-contamination and practical advantages with continued refrigeration during transport.