This study aimed to develop functional bread enriched with omega-3 fatty acids or silymarin. Nano sized complexes prepared in suspension by means of high-pressure homogenization were spray dried to obtain micron sized aggregated particles of omega-3 fatty acids and silymarin encapsulated with high amylose corn starch (HACS). These particles were incorporated into bread formulation at different amounts. Addition of particles up to 2.5% had no adverse effect on bread quality parameters and sensory properties. The particles remained intact in crumb, but partially destroyed in the crust. Additional amylase activity in the dough caused an increase in the rate of lipid oxidation and silymarin degradation during baking. The results of present study revealed that nano-encapsulation helps improving the thermal stability of heat labile bioactive compounds in bread at elevated temperatures.