The question of whether task performance is best achieved by domain-specific, or domain-general processing mechanisms is fundemental for both artificial and biological systems. This question has generated a fierce debate in the study of expert object recognition. Because humans are experts in face recognition, face-like neural and cognitive effects for objects of expertise were considered support for domain-general mechanisms. However, effects of domain, experience and level of categorization, are confounded in human studies, which may lead to erroneous inferences. To overcome these limitations, we trained deep learning algorithms on different domains (objects, faces, birds) and levels of categorization (basic, sub-ordinate, individual), matched for amount of experience. Like humans, the models generated a larger inversion effect for faces than for objects. Importantly, a face-like inversion effect was found for individual-based categorization of non-faces (birds) but only in a network specialized for that domain. Thus, contrary to prevalent assumptions, face-like effects for objects of expertise do not support domain-general mechanisms but may originate from domain-specific mechanisms. More generally, we show how deep learning algorithms can be used to dissociate factors that are inherently confounded in the natural environment of biological organisms to test hypotheses about their isolated contributions to cognition and behaviour.