The market for non-phthalate plasticisers (NPPs), such as adipates, citrates, phosphates, and carboxylates, has grown due to their low toxicity, but no studies have determined their metabolites during degradation processes in soil. This study evaluated the degradation of diethyl hexyl adipate (DEHA) and acetyl triethyl citrate (ATEC) in nonsterile soil, and the results were compared with those obtained from sterile soil, to determine whether microbial activity causes degradation in these NPPs. The analyses of these substances were performed using liquid chromatography coupled with quadrupole-Orbitrap high-resolution mass spectrometry (LC-Q-Orbitrap-HRMS). Plasticiser degradation followed a biphasic kinetic model, with a half-life time (DT50) of 9–12 days in non-sterile soil, but very slow in sterile soil (DT50 > 58 days). The degradation of target plasticisers in nonsterile soil resulted in the detection of eight metabolites of DEHA and ATEC, which were not detected in sterile soil. Among them, 4-[(2-ethylhexyl)oxy]-4-oxobutanoic acid (EHOBA), 4-((2-ethylhexyl)oxy)-4-oxo-1-carbonyl hexanoate (EHOCH), triethylcitrate (TEC) and N-acetyl glutamine (NAG) have been detected for the first time in this study. Most of these metabolites were detected after 14 days, increasing their concentration to 21 days, before completely degrading after 45 days. Nevertheless, mono–2-ethyl-5-hydroxyhexyl adipate (MEHHA), mono-2-ethyloxohexyl adipate (MEHOA), EHOCH, and diethyl citrate (DEC) were persistent in non-sterile soil (detected at 45 days) with an LD50 lower than their respective original molecules. Therefore, it is necessary to control the amount of these metabolites derived from the degradation of this type of plasticisers in the soil to avoid health risks, as they can end up in vegetables.