Abstract The development of effective and eco-friendly pesticides to manage mosquito vector larvae is a timely and crucial challenge nowadays. Insecticide resistance is on the rise, therefore plant-borne insecticides with multiple mode of action may represent promising candidates to control insect vectors. In the present work, we encapsulated selected essential oils (EOs) from Pimpinella anisum, Trachyspermum ammi and Crithmum maritimum into highly stable microemulsions (MEs) with the aim to develop effective and eco-friendly larvicidal formulations. MEs made with both single EOs and their mixtures were tested against 3rd instar larvae of Culex quinquefasciatus, assessing acute and chronic toxicity, emergence of adults, and their impact on non-target invertebrates, i.e., Daphnia magna, Tubifex tubifex and Eisenia fetida. All MEs were able to exert toxicity against mosquito larvae, with LC50 values in the ranges 1.45–4.01 ml L−1, along with high larval mortality and low percentage of hatched adults following short-term exposure to sublethal concentrations. Low or no mortality was observed on D. magna and E. fetida. Taken together, these results give new insights for the exploitation of plant-borne EOs as active ingredients of novel and reliable larvicidal products.