Abstract Background Limited information exists regarding changes in the size of respiratory and locomotor muscles in response to exercise training in the Thoroughbred racehorse. Objectives To describe and compare the responses of the respiratory and locomotor muscles to conventional exercise training and inspiratory muscle training (IMT). Study design Prospective randomised controlled trial. Methods Thoroughbred racehorses, in training for competition in National Hunt races, were recruited from two training establishments. Ultrasonographic images were obtained for selected muscles of the upper airway, diaphragm, accessory respiratory, and locomotor systems and their sizes measured. Examinations were performed at three timepoints: (A) when unfit, (B) following 12 weeks of conventional exercise training and (C) following 10–12 weeks continued training at race fitness. In addition, horses at yard 1 performed IMT, between timepoint B and C, and were randomly assigned into high‐load (treatment) or low‐load (control) group. Repeated measures models were constructed to compare the change in muscle measurements over time, and to investigate the effects of yard, previous airway surgery and IMT on the change in ultrasonographic size measurements obtained. Results Upper airway muscle size increased in response to conventional race training between timepoints A–C, and B–C. Diaphragm size increased in response to conventional exercise training between timepoints A and B. The diaphragm size of horses that undertook high‐load IMT was either maintained or increased, whereas diaphragm size decreased in horses that undertook low‐load IMT or no IMT between timepoints B and C. A significant interaction between gluteal muscle size and airway surgery status was observed, with greater gluteal muscle thicknesses measured in horses that had not previously undergone airway surgery (left gluteal 3.9%, p < 0.001 ; right 4.5%, p = 0.04 ). Main limitations Low number of horses underwent IMT. Conclusions Respiratory and locomotor muscles increase in size in response to conventional exercise training, with a further change in diaphragm size in response to inspiratory muscle training.