The phytotoxicity and eco-compatibility of essential oils (EOs) from Eucalyptus gunnii (EG) and E. pulverulenta ‘Baby Blue’ (EP), cultivated in Italy for their cut foliage, were investigated. Leaf micromorphology, EOs phytochemical characterization, and phytotoxicity were analysed. EP revealed a significantly higher oil gland density and a higher EO yield with respect to EG. In both EOs, 1,8-cineole was the major compound (~75%), followed by α-pinene in EG (13.1%) and eugenol in EP (7.5%). EO phytotoxicity was tested on both weeds (Lolium multiflorum, Portulaca oleracea) and crops (Raphanus sativus, Lactuca sativa, Lepidium sativum, Solanum lycopersicum, Pisum sativum, Cucumis sativus). EG EO inhibited germination of P. oleracea, R. sativus, and S. lycopersicum seeds (ranging from 61.5 to 94.6% for the higher dose used), while affecting only radical elongation in S. lycopersicum (ranging from 66.7 to 82.6%). EP EO inhibited germination of P. oleracea and R. sativus (ranging from 41.3 to 74.7%) and affected radical elongation of L. sativum and L. multiflorum (ranging from 57.4 to 76.0%). None of the EOs affected the germination and radical growing of L. sativa, P. sativum, and C. sativus. Moreover, EP EO was more active than EG EO in inhibiting α-amylase, a key enzyme for seed growth regulation. Brine shrimp lethality assay showed that both EOs are safe for aquatic organisms, suggesting their high eco-compatibility. The data collected provide useful information for future applications of these EOs in agriculture as safe and selective bioherbicides.