Between 1999 and 2020, there were twelve rapid alerts on dioxins in palm fatty acid distillate (PFAD) products, six of which were associated with hydrogenated palm fatty acid distillates (HPFADs). In palm oil refineries for food and feed, refined palm oil and PFADs can be processed into hydrogenated palm oil and HPFADs. This study investigated the effect of hydrogenation of palm oil products which contain OCDD and impact on the profiles of dioxins in palm oil products and on the toxic equivalent (TEQ) level. Palm oil and PFADs were spiked with octachlorodibenzo-p-dioxin (OCDD) and hydrogenated at different pressures, temperatures, and catalyst conditions. Initially, the concentrations of the lower-chlorinated dioxin congeners, some with a higher toxic equivalency factor, increased. Consequently, the TEQ levels increased and exceeded the regulatory limit. However, further hydrogenation extended the dechlorination of dioxins resulting in decreased TEQ levels. Optimisation of the hydrogenation process is required to reduce the risk of exceeding the limits on dioxins. • Hydrogenation of palm oil products affected the toxicity of dioxin congeners. • Octachlorodibenzo-p-dioxin (OCDD) dechlorinated during hydrogenation. • OCDD dechlorination initially formed congeners with higher toxicity. • Further hydrogenation reduced dioxin concentration and toxic equivalence level.