Most of the biodiversity studies in the South European Atlantic Shelf ecoregion are limited to shallow subtidal or intertidal habitats, while deeper reef habitats, also of relevant ecological importance, are particularly understudied. Macroalgal communities, associated fauna, and sea surface temperature were studied in deep reefs (25–30 m) at two locations in this ecoregion: Parcel, North of Portugal (41° N), and Tarifa, Southern Spain (35° N). Specifically, algal assemblages were assessed using biomass collection and associated ichthyofauna was assessed using visual census techniques using scuba. Seawater surface temperature was higher (>3 °C) in the southern region—Tarifa, compared to the northern region—Parcel. Our survey revealed 18 fish species and 23 algae species. The highest abundance of cold-water species (both macroalgae and fish species) was recorded in Parcel and warm-water species were dominant in Tarifa. In light of climate global trends, both regions might experience biodiversity shifts towards tropicalization. Current knowledge on their biodiversity is imperative to further evaluate potential shifts.