Value of the data •The data can provide insights on the link between the dynamics of free thymol concentration and the changes in fatty acids (FA) profile in quail egg yolk, both during chronic thymol dietary supplementation and after supplement withdrawal. •The data can be used for the establishment of optimal dosage and duration of thymol supplementation needed to achieve meaningful effects, as well as persistence of induced changes after supplement withdrawal. •The dataset could be used by the poultry industry for initiating exploratory studies for the use of thymol in dietary supplements. •The dataset could be used by other researchers for comparative studies for understanding in vivo thymol effects on a whole organism level. •The data can be used in the context of toxicological evaluation of chronic thymol dietary supplementation.