The Hibiscus sabdariffa (H. sabdariffa) belongs to the Malvaceae family, and originates from Africa. It is characterized by a high polyphenols content (e.g., quercetin and anthocyanins), and has recognized bioactivity, that makes this plant an interesting resource for possible addition of its extracts to dairy beverages and obtain functional beverages. Nonetheless, it may be observed that many of these phenolic compounds are not stable depending on the environmental conditions. In this work, we propose the use of nanostructured lipid carriers (NLC) as a carrier for the loading of H. sabdariffa extracts, for further incorporation in daily beverages. Polyphenols-enriched extracts from H. sabdariffa were obtained using two distinct extraction approaches: by (i) microwave-assisted extraction (MAE), or by (ii) pressurized liquid extraction (PLE). The obtained extracts were then loaded into NLC to obtain two distinct samples identified as: HS-MAE-NLC and HS-PLE-NLC. The developed nanoparticles were then incorporated into a dairy beverage for the production of fortified milks identified with the same names. The long-term stability, texture properties and in vitro release profile were evaluated. The results show that the fortified milks, HS-MAE-NLC and HS-PLE-NLC, were stable under stress conditions attributed to the enhanced stability provided by the protein content present in the milk. The in vitro release profile of quercetin and anthocyanins from NLC-enriched dairy beverage was more prolonged than the milk containing the non-loaded extract, fitting better to the Korsmeyers–Peppas model. From our results, NLC may be considered a potential approach to formulate photoprotective, anti-inflammatory, and antioxidant bioactives from H. sabdariffa adding the extracts into dairy beverages to increase their bioavailability, and bioactivity.