Searching for factors that reduce zearalenone (ZEN) toxicity is an important challenge in wheat production, considering that this crop is a basic dietary ingredient. ZEN, absorbed by cells, is metabolized into α-zearalenol and α-zearalanol, and this study focused on the function of manganese ions as potential protectants against the mycotoxins. Stress effects were invoked by an application of 30 µM ZEN and its derivatives. Manganese ions were applied at 100 µM, not stress-inducing concentration. Importance of the biomembrane structures in the absorption of the mycotoxins was demonstrated in in vitro wheat calli and on model membranes. ZEN showed the greatest and α-zearalanol the smallest stressogenic effect manifested as a decrease in the calli growth. This was confirmed by variable increase in antioxidant enzyme activity. Mn ions added to the toxin mixture diminished stressogenic properties of the toxins. Variable decrease in total lipid content and the percentage of phospholipid fraction detected in calli cells exposed to ZEN and its metabolites indicated significance of the membrane structure. An analysis of physicochemical parameters of model membranes build from phosphatidylcholine, a basic lipid in native membranes, and its mixture with the tested toxins made by Langmuir technique and verified by Brewster angle microscopy, confirmed variable contribution of ZEN and its derivatives to the modification of membrane properties. The order of toxicity was as follows: ZEN ≥ α-zearalenol > α-zearalanol. Manganese ions present in the hydrophilic phase interacted with polar lipid groups and reduced the extent of membrane modification caused by the mycotoxins.