Several indirect methods have been developed for the determination of 3-chloropropane-1,2-diol (3-MCPD) esters in fat matrices, but the variation between these methods leads to an uncertainty about the comparison of the results. All the indirect methods are based on the conversion of 3-MCPD esters into free 3-MCPD upon transesterification (either in acid or alkaline solution), its purification, derivatisation and instrumental analysis. In this study, major critical factors of the methodology, particularly transesterification, salting out and the choice of internal standard, were evaluated. 3-MCPD showed low stability under the conditions of alkaline transesterification (only around 40% recovery) affecting the sensitivity of the method. Furthermore, the results obtained within the first 1–2 min were 10–20% higher than those obtained at longer (5–10 min) transesterification time. A comparison of results obtained by using two different internal standards (free or esterified form of deuterated 3-MCPD) revealed a slight overestimation (7–15%) when free deuterated 3-MCPD was used, which may be possibly explained by the different behaviour of the both forms during alkaline transesterification. The use of different salts and pH values of the reaction medium during salting out step had a major impact on the results due to the formation of additional 3-MCPD. Other compounds, like glycidyl esters, present in oil samples may be converted to 3-MCPD during this step, however, the conversion was not complete and varied substantially (12–93%) in dependence on the pH value of the medium. The method based on acid transesterification showed better selectivity and robustness.