Venoms are biochemical arsenals that have emerged in numerous animal lineages, where they have coevolved with morphological and behavioural traits for venom production and delivery. In centipedes, venom evolution is thought to be constrained by the morphological complexity of their venom glands due to physiological limitations on the number of toxins produced by their secretory cells. Here, we show that the uneven toxin expression that results from these limitations have enabled giant centipedes to regulate the composition of their secreted venom despite having morphologically undifferentiated venom glands. We show that this control is likely achieved by the complex neuronal networks that innervate each venom gland subunit and is facilitated by morphological adaptations that circumvent the physiological evolutionary constraints on venom production. Our results suggest behavioural control over venom composition may be an overlooked aspect of venom biology and provide an example of how exaptation can facilitate evolutionary innovation and novelty.