The fortification of bread is considered an effective approach for improving its nutritional properties. However, the incorporation of free bioactive components into bread formulations may affect the overall quality of breads in different ways, depending on the sensitivity of bioactive components to baking factors. In this study, the incorporation of encapsulated vitamin C (ascorbic acid and its salts) and fish oil in breads was investigated for their stability and effect on bread quality. The combination of fish oil emulsions increased the retention of encapsulated ascorbic acid, calcium ascorbate, or sodium ascorbate in breads compared to that of the free non-combined vitamin. At the same time, the combination of vitamin gels increased the retention of docosahexaenoic acid (DHA) and decreased the lipid oxidation in breads compared to the non-combined encapsulated forms. The highest retention values of ascorbic groups, eicosapentaenoic acid (EPA), and DHA were about 70%, 88%, and 95% in breads after baking, respectively. There was the negative correlation between the ABTS radical scavenging capacity and peroxide value in breads. The specific volume of breads was improved by vitamin gels but reduced by fish oil emulsions. Their combination resisted individual impact on the specific volume of breads. The breads with combined ascorbic acid gels and fish oil emulsions showed similar textural properties to the control one. The functional bread with calcium ascorbate gel and fish oil emulsion had the highest moisture content of 45.87%. The inclusion of vitamin gels plus fish oil emulsion decreased free water but increased the bound water. Combining ascorbic acid gels with fish oil emulsions effectively reduced and masked the fishy flavor. The integration of encapsulation techniques and multi-nutrient fortification is proposed as an effective way to enhance the nutritional value and quality of functional bread through synergistic effects.