The objective of this paper was to determine the impact of a starter culture applied, storage time, pH changes, and the addition of glucose on the fatty acid composition of fermented soya milk. In model soya yoghurts, the following fatty acids were determined using a gas-chromatography-mass- spectrometer: lauryl acid (C12), palmitic acid (C16), palmitoleic acid (C16:1 n-9), margaric acid (C17), nonadecanoic acid (C19), oleinic acid (C18:1 n-9), vaccenic acid (C18:1 n-11), linoleic acid (C18:2 n-9, n-12), arachidic acid (C20), and α-linolenic acid (C18:3 n-9,n-12, n-15). The major acids in soya yoghurt were: linoleic acid (C18:2 n-9, n-12), oleinic acid (C18:1 n-9), palmitic acid (C16:0), and α-linolenic acid (C18:3 n-9, n-12, n-15). It was proved that the storage time had a significant impact on the fatty acid profile. No statistically significant impact of bacteria culture and addition of glucose were reported on the content of fatty acids under analysis. The addition of glucose significantly impacted the pH value and caused the biochemical activity of micro-flora to decrease; thus, there were no changes in the content of the acids studied.