Several wild bird and fish species across the Northern Hemisphere have been shown to episodically be thiamine deficient. This may lead to mass-mortality events, especially in offspring. To understand the mechanisms underlying thiamine deficiency we need a better understanding of the dynamics and somatic allocation of the vitamin. Here we focus on a common, ecologically and economically important species, that is, Atlantic cod (Gadus morhua), which has been suggested to be sensitive to thiamine deficiency. We sampled cod of varying sizes and maturity stages in a system where thiamine deficiency regularly occurs (i.e., Baltic Sea) and compare these with cod from the North Atlantic, where this deficiency has not been recorded. Results show that thiamine concentrations were tissue-specific. Concentrations in muscle and liver generally declined during growth and maturation, whereas concentrations in gonads increased. Of the total thiamine in a female's body, approximately 70% of the total pool was allocated to the gonads at the onset of reproduction, suggesting that micronutrients constitute a major investment when spawning. Free thiamine was the dominating vitamer in gonads and increased in proportion of total thiamine as gonads developed, whereas the muscle and liver's relative composition of vitamers was constant with thiamine diphosphate dominating. Transketolase activity and latency suggest that livers were saturated with thiamine and there was no evidence of ongoing thiamine deficiency. Likewise, thiamine concentrations were similar between areas with different histories of thiamine deficiency when accounting for differences in size and reproductive state, suggesting that thiamine statuses were comparable. We show that life cycle and tissue-specific dynamics in thiamine concentrations should be considered when assessing the thiamine status of a species. Furthermore, we discuss how specific life history traits related to spawning may put species at higher risk of thiamine deficiency.