Background: Fruit peels are generally underutilized byproducts of the food industry, although they are valuable sources of bioactive compounds. The aim of this study is to evaluate a new application for three Citrus peel EOs as bio-herbicides. Methods: After a micro-morphological evaluation of Citrus peels by SEM analysis, the phytochemical composition of the EOs of Citrus × bergamia Risso & Poit., Citrus × myrtifolia Raf., and Citrus limon (L.) Osbeck was characterized by GC/FID and GC/MS analyses. The in vitro phytotoxicity against germination and initial radical elongation of several crop and weed species was evaluated. Furthermore, the eco-compatibility of these EOs has been assessed by the brine shrimp (Artemia salina) lethality assay. Results: SEM analysis highlighted the morphometric differences of the schizolysigenous pockets among the peels of the three Citrus species. Oxygenated monoterpenes are the main constituents in C. × bergamia (51.09%), whereas monoterpene hydrocarbons represent the most abundant compounds in C. × myrtifolia (82.15%) and C. limon (80.33%) EOs. They showed marked and selective phytotoxic activity in vitro, often at very low concentration (0.1 μg/mL) against all plant species investigated, without showing any toxicity on Artemia salina, opening the perspective of their use as safe bio-herbicides.