Patients with Achilles tendinopathy exhibit altered tendon mechanics, including changes in the sliding behaviour of Achilles tendon (AT) subtendons and variations in material properties. These individual mechanical alterations influence the AT’s response to load and the resulting strains, which are critical for understanding the mechanisms underlying Achilles tendinopathy and promoting effective recovery. The goal of this study was to develop an optimization routine to determine 1) patient-specific AT mechanics, representing the altered sliding mechanisms and 2) patient-specific material properties of the AT, thereby offering a more individualized depiction of the tendon’s response under load. Thirteen patients with Achilles tendinopathy were imaged at rest using three-dimensional freehand ultrasound. The images were manually segmented to create finite element models with patient-specific AT shapes, which also incorporated the twisted geometry of the subtendons. The optimization routine was informed by various in vivo experimental data, including AT elongations estimated during sub-maximal voluntary isometric contraction (measured via three-dimensional freehand ultrasound) for material coefficient estimation, as well as localized AT differential displacement (measured via ultrasound speckle tracking) for friction coefficient estimation. Additionally, patient-specific maximal voluntary isometric contraction (MVIC) force estimations were integrated into the model. This optimization process identified patient-specific material and friction coefficients for the finite element models, enabling the closest possible alignment with experimental observations. By incorporating altered tendon properties, such as subtendon sliding and material characteristics, the routine provides a tool for future applications which aim to gain a comprehensive understanding of the individualized AT response to load and offer valuable insights for managing Achilles tendinopathy.