The present study has been inspired by the growing need for rigorously controlling the nutritional quality and safety of food products. The impact of application in the food industry on fatty acids composition, trans-fatty acids (TFAs), and conjugated linoleic acid (CLA) profiles were investigated in a highly consumed candy byproduct of sesame seed (chamia) in comparison to fresh sesame seed oil (SSO) and heated SSO under simulated frying experiments. The effect of treatment on SSO was studied by determining the TFA and CLA changes. Results showed significant differences between the two byproducts in TFA and CLA amounts. Total TFAs were found to be significantly higher in chamia than fresh SSO (1.31 versus 0.066%, respectively; p < 0.05) and even higher than all heated SSO from 2 to 10 h at 180 °C (1.31 versus 0.33%, respectively; p < 0.05). A significant linear relationship was found between trans-monounsaturated fatty acid (MUFA), trans-polyunsaturated fatty acid (PUFA), and total TFA and the time of processing, with a correlation coefficient (R(2)) greater than 0.9 for TFA and PUFA, with a higher correlation assigned to PUFA (r = 0.988; p < 0.001), followed by TFA (r = 0.959; p < 0.01) and MUFA (r = 0.844; p < 0.05). Principal component analysis of the fatty acid (FA) profiles showed discrimination between chamia and both fresh and heated SSO. A high stability of SSO against isomerization reactions as compared to their chamia sample counterpart has been noted. These findings suggest that the food industry engenders relatively higher changes in fatty acid configurations than the frying process.