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Systematic tool use is a central component of the human niche. However, the timing and mode of its evolution remain poorly understood. A newly developed method for the analysis of muscle recruitment patterns (Validated Entheses-based Reconstruction of Activity - V.E.R.A.) has recently been experimentally shown to provide clear and reliable evidence of habitual activity during life from skeletal remains. It is thus ideal to investigate the emergence of tool-related behaviors in the human fossil record. Here, we investigate this question by applying V.E.R.A. to the attachment proportions of thumb (first metacarpal) muscles considered crucial for tool use, in combination with a geometric morphometric analysis of bone shape. Our sample comprises modern humans, extant great apes, Neanderthals, Homo naledi, three Australopithecus species (A. afarensis, A. africanus and A. sediba) and a taxonomically unassigned fossil hominin from Swartkrans, South Africa. Results show that modern humans are distinct from extant non-human great apes in the recruitment patterns of the thumb muscles examined, as expected. Importantly, all hominins except A. africanus exhibit human-like thumb muscle use irrespective of the overall shape of their first metacarpal. This pattern supports habitual tool-related behaviors in these early taxa—excluding A. africanus—despite their lack of skeletal adaptations for efficient tool use observed in the first metacarpals of later Homo. Our findings strongly suggest habitual tool use by early hominins, and indicate an early, mosaic establishment of this behavior among Australopithecus taxa, preceding the evolution of tool-related biomechanical adaptations of the hominin hand and consistent with recent archaeological discoveries.