Abstract Unilateral lesions of the forelimb sensorimotor cortex and motor skills training interact to enhance synaptic plasticity in layer V of the motor cortex contralateral to the lesion in male rats. In this study, we assessed the metabolic correlates of these synaptic changes by quantifying the number and size of mitochondria in synaptic axonal terminals with perforated or non-perforated post-synaptic densities (PSDs) and single or multiple post-synaptic contacts. The number of synaptic mitochondria per neuron was significantly greater in rats with lesions. Neither manipulation affected mitochondrial size or number of mitochondria per synapse. Independent of experimental condition, terminals with perforated PSDs had more mitochondria than those with non-perforated PSDs and, among those with non-perforated PSDs, terminals with multiple synaptic contacts had more mitochondria than those forming single synapses.