The Rapid Alert System for Food and Feed (period 1999–2014) reported exceeding levels of dioxins (polychlorinated dibenzo-p-dioxinsand dibenzofurans (PCDD/Fs)) in palm oil by-products, such as palm fatty acid distillate (PFAD) and hydrogenated palm fatty acid distillate (HPFAD), but not in crude and refined palm oil. The aim of the present study was to gain insight into the occurrence and congener profiles of dioxin contamination during industrial processing of crude palm oil into refined oil and its by-products PFAD and HPFAD via analysis of individual congener concentrations. In total, 1217 samples from an industrial process were collected at four different points, crude palm oil at delivery (N = 202), fresh bleaching earth before bleaching (N = 84), PFAD after deodorising palm oil (N = 553), and HPFAD after hydrogenation of PFAD (N = 378). Congener profiles were analysed by GC-HRMS, and toxic equivalent (TEQ) levels were calculated using toxic equivalence factors (TEF) of WHO2005 to assess non-compliance to legal limits. All dioxin levels in crude palm oil samples were far below the action limit. All dioxin levels in fresh bleaching earth were in compliance with the maximum level. For the by-product samples, such as PFAD, 0.6% exceeded the action level, but all were below the maximum level (ML). However, for 1.3% of the HPFAD samples, the TEQ level exceeded the ML.In-depth analysis of the congener profiles revealed that after the hydrogenation step, the concentration of the lower chlorinated congeners in the HPFAD samples was higher than in the PFAD samples. The hydrogen atoms possibly replaced the chlorine atoms during hydrogenation. As these lower chlorinated congeners have a higher TEF, when they are regulated, their contribution to the calculated TEQ is higher, which resulted in some HPFAD samples exceeding the legal limit. Further research is needed to obtain insight into the changes in PCDD/F congener profiles during the hydrogenation of palm oil products.