Wipe sampling is widely used for microbiological control purposes. Sanitary and chemical studies also include analysis of samples wiped from the work surfaces during routine and periodic working conditions safety inspections at chemical facilities. The analysis also allows assessing the toxicity and hazard of items/structures that could be in contact with highly toxic substances. This study aimed to investigate the capabilities and limitations of the surface wipe sample analysis method in control of residual contamination of equipment and building structures of a former chemical weapons destruction facilities (CWDF) with sulfur mustard and O-isobutyl-S(2-diethylaminoethyl) methylphosphonothioate (VR), as well as their degradation products. Gas chromatography with tandem mass spectrometry (GC-MS/MS) enabled identification of the sulfur mustard markers, high-performance liquid chromatography with tandem mass spectrometry (HPLC-MS/MS) allowed identifying VR markers. An assessment of the matrix influence on the results of GC-MS/MS and HPLC-MS/MS analysis was carried out. The matrix effect was established to affect the results the most in case of HPLC-MS/MS analysis: for GC-MS/MS analysis of target substances, the matrix factor averaged at 60–80%, for HPLC-MS/ MS it was less than 40%. The average percent sulfur mustard recoveries from three types of surfaces (PVC tiles, laminate and metal plates) was 9 ± 2%, 0.13 ± 0.02% and 0.10 ± 0.03%; in case of VR, the recoveries was 2.7 ± 0.5%, 11.8 ± 0.3% and 0.8 ± 0.1%, respectively. The limits of detection for sulfur mustard by GC-MS/MS and VR by HPLC-MS/MS were established at 0.001 MPL and 0.02 MPL, respectively. The developed approaches were applied to the analysis of wipe samples from the surfaces of the equipment and engineering structures of the former CWDF.