This work presents an innovative strategy to enhance the nutritional quality—specifically the retention and delivery of polyphenols and carotenoids—of plant-based foods. Bioactive compounds extracted from tomato pomace (skins and seeds) were concentrated, encapsulated using a 1:1 maltodextrin–inulin blend, and spray-dried into powders that were incorporated into a spreadable avocado matrix. Focusing on a spreadable avocado matrix, the study explored how integrating these encapsulated compounds—rich in health-promoting carotenoids—could improve both shelf stability and nutritional properties. Multiple preservation techniques were tested, including conventional thermal processing (CT), ultrasound treatment (US), and high hydrostatic pressure (HHP), to assess their influence on the stability of bioactive content, antioxidant activity, and microbial safety during refrigerated storage. Encapsulation played a crucial role in protecting sensitive compounds by reducing their degradation by 5-25%, supporting their retention over time and contributing to a more stable antioxidant profile throughout the product’s shelf life. Among the preservation methods, HHP demonstrated a synergistic effect, improving microbial safety, reducing 2–4 log CFU/g without the thermal degradation commonly associated with conventional heat treatments. This approach also preserved a greater proportion of phenolic compounds (~1.35 g GAE/kg), underscoring the advantages of non-thermal technologies in maintaining nutritional quality. In contrast, thermal treatment showed a noticeable reduction in phenolics (~40%), highlighting the trade-offs between microbial control and nutrient preservation. The integration of encapsulated ingredients derived from horticultural by-products offers a dual benefit—improving food quality while advancing sustainable practices through the upcycling of agro-industrial waste. This study underscores the promise of combining encapsulation and gentle preservation techniques to create clean-label, functional foods aligned with consumer demand for health, sustainability, and transparency.