The soil ecosystem is composed of a mixture of living organisms and non‐living matter as well as the complex interactions between them. In the past 100 years or so, agricultural soil ecosystems have been strongly affected by agricultural practices such as tillage and the use of pesticides and fertilizers, which strongly affect soil nutrient composition, pH and biodiversity. In modern pest management, however, the focus is gradually shifting from crop production through agricultural practices to soil ecosystem protection. In this review we discuss how the underground chemical signals secreted by plant roots play a role in keeping the soil ecosystem in balance and how they affect plant fitness by shaping the root biome, increasing nutrient availability, promoting symbiosis, and attracting beneficial organisms and repelling harmful ones, including other plants. We review a number of fascinating cases, such as signaling molecules with dual, positive and negative, functions and bacterial quorum sensing mimicking molecules. Finally, examples of how these compounds can be exploited in modern pest management are reviewed, and the prospects for future developments discussed. © 2019 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.