Our understanding of the immediate effects of exercise on Achilles free tendon transverse morphology is limited to single site measurements acquired at rest using 2D ultrasound. The purpose of this study was to provide a detailed 3D description of changes in Achilles free tendon morphology immediately following a single clinical bout of exercise. Freehand 3D ultrasound was used to measure Achilles free tendon length, and regional cross-sectional area (CSA), medio-lateral (ML) diameter and antero-posterior (AP) diameter in healthy young adults (N=14) at rest and during isometric muscle contraction, immediately before and after 3×15 eccentric heel drops. Post-exercise reductions in transverse strain were limited to CSA and AP diameter in the mid-proximal region of the Achilles free tendon during muscle contraction. The change in CSA strain during muscle contraction was significantly correlated to the change in longitudinal strain (r=-0.72) and the change in AP diameter strain (r=0.64). Overall findings suggest the Achilles free tendon experiences a complex change in 3D morphology following eccentric heel drop exercise that manifests under contractile but not rest conditions, is most pronounced in the mid-proximal tendon and is primarily driven by changes in AP diameter strain and not ML diameter strain.