The aim of the study was to evaluate the impact of selected fatty acids: palmitic, stearic or oleic on functional properties of cassava and wheat starches. Effectiveness of complexation procedure was evaluated by determination of complexing index, lipids content and fatty acid composition. Native starches and their complexes with fatty acids were analyzed for water binding capacity and solubility in water, in vitro digestibility, pasting characteristic and rheological properties. On the basis of the obtained results it was found that values of complexing index values for both starches complexed with oleic acid were remarkably higher than those determined in palmitic or stearic counterparts. Starches complexation with fatty acids resulted in a significant increase in the percentage share of used fatty acid in total fatty acid composition. Presence of oleic acid in cassava starch significantly limited its water binding capacity and solubility in water. Complexation with all fatty acids used in the study resulted in an increase in final viscosity and rheological stability of cassava starch pastes. Wheat starch complexes with fatty acids were characterised by higher pasting temperatures as compared to non-complexed counterpart, with the greatest effect observed for starch–oleic acid complex. In most cases complexation of starches with fatty acids contribute to an increase in contents of resistant starch fraction. Analysis of rheological model parameters revealed that procedure of oleic acid complexation increased by twice the values of consistency coefficient, and significantly decreased flow index of both wheat and cassava starches.