Natural herbicides based on essential oils (EOs) extracted from aromatic plants are gaining relevance in contemporary agriculture. Due to their allelopathic properties, they have an inhibitory effect on the germination and growth of different species, having, in general, the advantage of high specificity. For this reason, the analysis of the effects of these natural compounds on noxious weeds is continuously increasing. In the present study, three commercial EOs extracted from Mentha piperita L., Thymbra capitata (L.) Cav. and Santolina chamaecyparissus L. were tested on two invasive weeds with an increasing presence in southern Europe, Erigeron bonariensis L. and Araujia sericifera Brot. Five concentrations (0.125, 0.25, 0.50, 1 and 2 µL mL–1) were tested in a randomized manner for each essential oil and five replicates with 20 seeds each for E. bonariensis and 10 replicates with 10 seeds each for A. sericifera. Two higher concentrations of 4 and 8 μL mL–1 of the three EOs were applied with irrigation on the plants of the two species at the vegetative growth stage. The number of replicas for each treatment and species was 7. The results obtained confirmed the significant inhibitory effects on seed germination and early seedling development, especially in E. bonariensis; of the three EOs, peppermint had the strongest effect, completely preventing germination in both species. Multivariate analysis, performed on several morphological traits scored after one month of treatment in young plants, showed a different pattern: the highest inhibition was recorded in A. sericifera and the greatest reduction in growth in the treatment with the highest dose of Santolina EO. The results obtained revealed the efficacy of these natural compounds and the specificity of their toxicity according to the species and stage of development.