Performing pre‐deacidification using short‐path distillation at high temperatures and vacuum levels is a general application for fats and oils with high free fatty acids (FFA) to reduce their FFA contents to reasonable levels before steam distillation or neutralization. This study aims to determine the changes in 3‐chloropropane‐1,2‐diol esters (3‐MCPDE), glycidyl esters (GE), and diglyceride (DG) as well as the losses in tocopherols during this process. A bleached hazelnut oil having 12.10% FFA content was distilled using a molecular distillation unit at 200 °C, 220 °C, and 240°C temperatures and 0.25, 0.5, 1, and 2 mbar absolute pressures. The target was to reduce FFA content to less than 2% with minimum tocopherol loss. The results showed that considerable removals in FFA and GE contents were achieved by increasing the temperature and vacuum, while fewer decreases were detected in 3‐MCPDE and DG concentrations. Tocopherols were dramatically decreased by temperature rising, therefore, the lowest temperature (200°C) and absolute pressures (0.25–0.5 mbar) might be suitable for pre‐deacidification of hazelnut oil, where the distilled oil contained 1.78%–1.90% FFA, 243.11–286.76 mg kg–1 tocopherol, 0.50–0.55 mg kg–1 3‐MCPDE, 0.03–0.05 mg kg–1 GE and 4.00–4.22 mg kg–1 DG.Practical Application: Vegetable oils with high free fatty acid (FFA) contents are generally subjected to physical refining to avoid considerable refining loss. However, high temperatures applied to vegetable oils during physical refining result in the formation of 3‐MCPDE&GE, and the loss of some nutrients, such as tocopherols. These adverse effects can be reduced through application of lower temperatures and shorter time during physical refining. This can be applied after the FFA contents of the oils are decreased to reasonable levels (less than 2%) by distillation (pre‐deacidification) before the deodorization. Although this technique has been implemented in many plants, there is almost no information on the effects of applied conditions on 3‐MCPDE and GE and some other minor constituents. This manuscript explains the changes in these compounds during the pre‐deacidification of hazelnut oil by molecular distillation. Suitable distillation conditions were also suggested, which would be very useful for industrial refining plants.