As inter-limb asymmetries can be associated with higher injury risk, we aimed to investigate their role in Achilles tendinopathy patients. In Achilles tendinopathy patients (n = 41), we assessed inter-limb asymmetries of mechanical, material, and morphological musculoskeletal properties and function and how those were affected by 12 weeks of exercise intervention (high-load protocol, n = 13; Alfredson protocol, n = 11). Moreover, we assessed whether asymmetry reductions correlated with improved Patient-Reported Outcomes (VISA-A score). At baseline, tendinopathic tendons demonstrated lower tendon force (p = 0.017), lower tendon stress (p < 0.0001), larger tendon cross-sectional area (CSA) (p < 0.001), and increased intratendinous (p = 0.042) and tendon overall (p = 0.021) vascularization. For the high-load group, PRE-to-POST asymmetry comparisons revealed an asymmetry increase for the counter-movement jump (CMJ) (p = 0.034) and PRE-to-POST VISA-A score improvements correlated with CSA asymmetry reductions (p = 0.024). Within the Alfredson group, PRE-to-POST VISA-A score improvements correlated with CMJ asymmetry reductions (p = 0.044) and tendon stiffness asymmetry increases (p = 0.037). POST-to-POST in-between group comparisons revealed lower asymmetry in the high-load group for tendon elongation (p = 0.021) and tendon strain (p = 0.026). The tendinopathic limb differs from the asymptomatic limb while therapeutic exercise interventions have little effect on asymmetries. Asymmetry reductions are not necessarily associated with tendon health improvements.