This study evaluates the performance and storage stability of functional extrudates enriched with natural additives, utilizing advanced food engineering and processing techniques. Essential oils from oregano, rosemary, hypericum, and chamomile were incorporated in both free and encapsulated forms using electrohydrodynamic processing, spray drying, and freeze drying, and added to the food matrix through extrusion processing. The encapsulated additives demonstrated superior retention and controlled release of bioactive compounds, with spray-dried agents achieving the highest total phenolic content (1.66 mg GAE/g) post-extrusion. During storage, these extrudates exhibited enhanced stability with low degradation rate constants (1.90×10⁻³ days⁻¹ at aw=0.33, 25°C, over 240 days). The bioactive extrudates maintained remarkable stability in terms of hardness and colour change, with hardness inversely correlated to moisture content. These findings highlight the potential of using encapsulation and extrusion processing to create stable, naturally bioactive food products, reducing dependence on synthetic additives. The research underscores the integration of emerging technologies in food science to enhance the stability and delivery of essential oils, supporting the development of sustainable and health-promoting food systems.