The bioactive hydrolysis products of glucosinolates, particularly the isothiocyanates, can be used to control soil pests and weeds by incorporating glucosinolate-containing plant material in soil—a practice known as biofumigation. The fate of glucosinolates and their hydrolysis products in soil determines both the efficacy and environmental impact of biofumigation. Knowledge of the processes by which these compounds are sorbed, degraded or otherwise lost from the soil is fundamental to developing effective, but environmentally benign biofumigation strategies. Effective biofumigation relies on maximum hydrolysis of the glucosinolate in the plant tissue to generate high isothiocyanate concentrations in the soil after incorporation. This is favoured by maximum cell disruption, by addition of water, and a high soil temperature. Residual glucosinolates are very weakly sorbed, readily leached and are microbially degraded and mineralised in soil. In contrast, isothiocyanates are strongly sorbed by the organic matter in soil, react strongly with nucleophilic groups present in soil, and are prone to volatilization losses in addition to microbial degradation and mineralisation. These loss processes are influenced by soil type, water content and temperature. Using appropriate incorporation strategies, sufficiently high isothiocyanate concentrations (>100 nmol g⁻¹) can be achieved in soil using biofumigation for effective suppression of susceptible pests. The relatively rapid sorption and degradation of the isothiocyanates in the period of days after incorporation minimizes the risks of persistence in the environment or leaching. Biofumigation is therefore a promising technique which can be further developed to form part of IPM (Integrated Pest Management) strategies to reduce reliance on synthetic pesticides with minimal unintended impacts on the environment.