Summary Crude fats and oils may have high free fatty acid (FFA) content depending on raw material quality and processing conditions. Their refining is always a challenge due to refining loss and the formation of some process contaminants such as 3‐monochloropropane‐1,2‐diol esters (3‐MCPDE), and glycidyl esters (GE). In this study, crude hazelnut oil having 12.10% FFA was degummed, bleached, and pre‐deacidified by a molecular distillation (MD) unit before neutralisation and deodorisation. Changes in FFA, diglyceride(DG), 3‐MCPDE, GE, and tocopherol contents were monitored. Almost no changes were detected in FFA and DG contents during degumming and bleaching while the latter resulted in the 3‐MCPDE formation and GE reduction. Some tocopherol losses were also observed after these steps. On the other hand, a huge amount of FFA was distilled (from 12.10% to 1.71%) by the MD process performed at 200 °C, 0.25 mbar, as well as with a 53.6% loss of tocopherol. The samples were then subjected to deodorisation before (MD‐PHY) and after neutralisation (MD‐CHE) at 230 °C under 2 mbar absolute pressure for 2, 4, and 8 h. While some 3‐MCPDE and GE formations were detected during MD‐CHE, there were almost no formations in these contaminants after MD‐PHY. When the bleached oil having 12.10% FFA was also directly deodorised at given conditions, no formations but some reductions in 3‐MCPDE and GE contents of the oils were determined, possibly because of esterification of FFA with DGs that are an important precursor of these contaminants.