Environmental meta-metabolomics consider studying mixtures containing endogenous and xenobiotic metabolites, issued from the application of anthropogenic compounds to an environmental matrix. Our main research aim is to develop a Chromatography-Mass Spectrometry-based meta-metabolomics approach as an alternative tool for the evaluation of pesticides’ environmental fate and impact. This approach named “Environmental Metabolic Footprinting” consists of comparing meta-metabolomes of control and pesticide-spiked environmental matrix for several defined time points, in order to determine matrix’ “resilience time”. This considers the recovery of sample’s biological system by comparing these meta-metabolomes, using statistical analysis. Moreover, this approach aims to determine endogenous biomarkers, in order to understand the biological impact of the applied pesticide. Several technical issues may affect conclusions built on statistical analysis of LC-MS data. Ion suppression phenomenon is one of these issues, occurs in the Electrospray Ionization source. This phenomenon consists of suppressing the signal of a compound due to an ionization competition with another co-eluted molecule, which may originates from xenometabolome. It may leads to consider several non-significant molecular features as markers of discrimination. We have observed this phenomenon in one of our applications. In fact, pesticide-derived xenometabolites suppressed the signal of some co-eluted endometabolites, which could be considered as potential markers of discrimination. Here, we aim to exploit this case by analyzing LC-QToF data and statistical results, in order to notice this potentially recurrent issue in metabolomics, and the importance of the awareness about Mass Spectrometry fundamentals to assure reliable conclusions.