Globally, there is growing concern regarding the effects of the increasing anthropogenic pressures in marine communities. Artificial structures such as marinas and aquaculture facilities serve as invasion hotspots; hence, monitoring fouling communities on these structures can be valuable for detecting new invasions. In the current study, 24 settlement PVC plates were deployed for three months to compare the recruitment ability of these two artificial environments along the south coast of the offshore island of Madeira (NE Atlantic). The results showed higher variations in the species richness between regions (SW vs. SE) than between artificial habitats (sea-cages vs. marinas), although the community composition differed. Cnidaria and Bryozoa were the most representative groups in the aquaculture systems, while Bryozoa and Chordata were in the marinas. A sum of 18 NIS was recorded for the study, accounting for between 21.88% and 54.84% of the total number of species in the aquaculture facilities and marinas, respectively. The higher NIS percentage from the marinas was even more explicit in the SE coast, where Cradoscrupocellaria bertholletii, Parasmittina alba, and Botrylloides niger distinctly dominated fouling populations. The results suggest that at least some particular NIS previously reported in the studied marinas successfully colonized sea-cages. Future assessments need to address the potential role of aquaculture facilities as drivers for the secondary spread of NIS. Additionally, two new records are considered for Madeira: Eudendrium capillare and Ericthonius punctatus.