Waterlogging increasingly threatens global crop production, particularly affecting major crops like wheat, barley, and maize at all growth stages. Although research on oat tolerance to waterlogging is limited, there is evidence that oat may be a suitable alternative crop due to its resilience and ability to maintain yields despite nutrient imbalances caused by waterlogging. However, it remains uncertain how oat responds to changes in soil micronutrient availability during periods of waterlogging. Therefore, this study aims to investigate whether (1) micronutrient toxicities or deficiencies are induced during waterlogging, (2) the timing of the flooding event is relevant for the expression of a possible nutrient imbalance, and (3) micronutrient toxicities/deficiencies affect yield performance. In order not to exclude possible varietal differences, three oat varieties were grown in large-scale containers and exposed to 14 days of waterlogging at either BBCH 31 or BBCH 51. Although early but not late waterlogging was effective in reducing dry weights, especially in white oat, yield performance, as reflected by the harvest index, was not affected at all. While early waterlogging increased Mn and Fe concentrations in all oat varieties, they were well below toxic level. In contrast, Cu concentrations in white oat dropped below the deficiency threshold levels. Zinc status, however, remained completely unaffected in all oat varieties. After late waterlogging, only Mn accumulated to concentration in the toxicity range, but only in white and yellow oat; all other micronutrients remained in a sufficient range From these results we conclude, that although micronutrient imbalances occurred under waterlogging regardless from its timing, which may explain the transient reduction in dry weight of white oat, the yield of all tested oat varieties was ultimately unaffected. It can therefore be assumed that at least the oat varieties tested have a high regeneration potential and also show a high tolerance to transient micronutrient imbalances.