Three tree species (Wild olive, Stinkwood and Cape Holy) and a shrub (Dovyalis caffra) were each potted in 20 L pots in order to evaluate the effect of 1,3,5-trinitrotoluene (TNT)-contaminated soil on vegetation. TNT contamination was established by dissolving flake TNT in acetone at 300 and 600 mg per kilogram soil concentrations. One pot for every species was left uncontaminated as control elements. A set of 16 samples, four contaminated, four uncontaminated aerial parts and their corresponding soils, were gathered. These were processed and subjected to a solid phase extraction method to isolate analytes of interest. A laboratory analytical method was applied using ultra-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UPLC-qTOF MS). For the UPLC-qTOF MS a gradient for the mobile phase was found which allowed the profiling and separation of metabolites in the aerial parts of the vegetation. This method allowed identification and quantification of major changes caused by TNT contaminated soil on vegetation. The Synapt High Definition Mass Spectrometer SYNAPT HDMS G1 was operated using the electrospray ionisation (ESI) technique in both positive and negative mode. A clear comparison of profiles was achieved and this has been demonstrated by the distinct newly-formed metabolites in the TNT contaminated vegetation understudy. The results have also shown that the chlorophyll region in the contaminated profile was also affected by the uptake of TNT degradation products. This has been observed in the contaminated profiles of Wild olive, Stinkwood and Cape Holly extracts indicating enhanced nutrient availability.