The extensive use of chemical pesticides leads to risks for both the environment and human health due to the toxicity and poor biodegradability that they may present. Farmers therefore need alternative agricultural practices including the use of natural molecules to achieve more sustainable production methods to meet consumer and societal expectations. Numerous studies have reported the potential of essential oils as biopesticides for integrated weed or pest management. However, their phytotoxic properties have long been a major drawback for their potential applicability (apart from herbicidal application). Therefore, deciphering the mode of action of essential oils exogenously applied in regards to their potential phytotoxicity will help in the development of biopesticides for sustainable agriculture. Nowadays, plant physiologists are attempting to understand the mechanisms underlying their phytotoxicity at both cellular and molecular levels using transcriptomic and metabolomic tools. This review systematically discusses the functional and cellular impacts of essential oils applied in the agronomic context. Putative molecular targets and resulting physiological disturbances are described. New opportunities regarding the development of biopesticides are discussed including biostimulation and defense elicitation or priming properties of essential oils.