Mid-portion Achilles tendinopathy (MAT) adversely affects free Achilles tendon (AT) structure and composition. However, it is not known how these pathological alterations associated with MAT change the normal three-dimensional (3-D) morphology of free AT at rest and under load throughout the entire free tendon length. Here, we used 3-D ultrasound to examine the effect of unilateral MAT on free tendon 3-D morphology [length, cross-sectional area (CSA), anteroposterior (AP) diameter and mediolateral (ML) diameter] and volume at rest and during a submaximal (50%) voluntary isometric plantarflexion contraction bilaterally in individuals with unilateral MAT (n = 10) compared with a matched healthy control group (n = 10). The tendinopathic free AT had a greater CSA relative to the control tendons along the entire tendon length, which was mainly driven by a greater tendon AP diameter. Under load, the tendinopathic tendon experienced greater longitudinal and transverse strains than the control tendons. In contrast to the control tendons, which experienced a reduction in tendon CSA and ML diameter, bulged along the AP axis and behaved isovolumetrically under load, the tendinopathic tendon experienced a reduction in tendon CSA, AP diameter and ML diameter and an overall volume reduction. Overall, these findings suggest that the magnitude of longitudinal strain and volume change and the corresponding magnitude and direction of transverse strain under load are altered in MAT compared with normal tendon. These findings are indicative of a fundamental reorganization of the tendon matrix and alterations in tendon fluid content and distribution under load in tendinopathic tendon.