To gain a better understanding of the mechanisms through which a chemical exerts toxicity, a deeper insight is needed regarding the physiological processes that take place during a toxic stress. This issue can have important benefits for risk assessment, because it can contribute to a better interpretation of toxicity data. Here, we study the physiological mode of action of three different compounds (cadmium, carbendazim, and pentachlorobenzene) with an experimental data–based approach using whole life-cycle toxicity data from the nematode Acrobeloides nanus. We use a process–based model, based on the dynamic energy budget theory, to study the fluxes of energy related to physiological processes and their variation throughout the life cycle. With this approach, we unravel the physiological modes of action based on resource allocation, and we model the effects of the different modes of action at the population level. The mode of action of carbendazim was through a decrease in assimilation, with an additional effect on the production of reactive oxygen species (ROS). Cadmium increased the costs of growth, with an extra effect on ROS production, and pentachlorobenzene decreased assimilation. We compared the present results with those of previous studies using the nematode Caenorhabditis elegans, and we found that the modes of action for the three compounds differed from those found in A. nanus, showing that the life-history characteristics of each organism have a clear influence on the resulting modes of action. This highlights the importance of the interactions between a chemical and the biological characteristics of the organism in determination of the resulting physiological modes of action.