Analyte range of gas chromatography–mass spectrometry (GC–MS), widely used in environmental analysis, can be significantly broadened by derivatization. Silyl derivatives have improved volatility and thermal stability, chromatographic and mass spectrometric behaviors, and thus detection, structural elucidation and quantification. However, silylation use is often hindered by the stability of generated derivatives and the need to optimize silylation conditions. In this study, we optimized the derivatization conditions for 70 selected contaminants of emerging concern (CEC) using chemometrics approaches. N-methyl-N-(trimethylsilyl) trifluoroacetamide (MSTFA), N, O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) and BSTFA + 1 % trimethylchlorosilane (TMCS) were investigated, among which the latter gave the best yield. CEC were grouped in three derivatization protocols: 60 °C/45 min, 70 °C/90 min, and 70 °C/45 min. The short- and long-term stability of the CEC-trimethylsilyl (TMS) derivatives, i.e. for 28 days and up to 20 weeks were examined in a solvent and artificial wastewater (AWW) extract at 25 °C, 4 °C and − 18 °C, and during repeated five freeze-thaw (F/T) cycles, at two concentration levels: 100 μg/L and 1000 μg/L. Except for TMS derivatives of shikimic acid (SHA), quinic acid (QA) and sulfanilamide (SFA), the remaining derivatized compounds were stable in solvent (EtAc) for 28 days. In AWW extract, TMS derivatives of citric acid (CA), 17β-estradiol (E2), estriol (E3) and 17α-ethinyl estradiol (EE2) were unstable at 25 °C and 4 °C. Within up to 20 weeks, only the TMS derivatives of CA, meso-erythritol (ERY) and bisphenol BP (BPBP) were unstable. The most significant hydrolytic breakdown was observed during repeated F/T cycles. After three cycles, ≤ 20 % of the initial concentration of six and nine CEC-TMS derivatives had degraded in solvent and AWW extracts, respectively. According to the deep statistical comparison (DSC) approach, the most prominent degradation was observed for TMS derivatives of E2, CA, 9-hydroxyfluorene (9-HF), estrone (E1) and trans-3′-hydroxycotinine (T3HC) in solvent; E2, CA, 9-HF, E3 and E1 in AWW extracts and ERY, E2, CA, 9-HF and E1 in both matrices. Finally, the sample concentration of CEC accounted for most of the measurement uncertainty (MU).Based on our findings, we recommend the derivatized samples to be stored at −18 °C for up to 20 weeks to ensure the stability of their TMS derivatives. Sample freezing and thawing of not more than twice is allowed to maintain ≥80 % of the initial CEC-TMS concentration.