Wholemount, 3-dimensional (3D) tissue imaging holds significant promise for analyzing heterogeneous musculoskeletal tissues, such as knee joints, that demand time- and labor-intensive processing using traditional histological methods. Current musculoskeletal clearing protocols rely on either solvent-based tissue clearing, which substantially alters the size and architecture of cleared tissues, possibly compromising downstream quantification and perhaps more importantly reducing signal from endogenous fluorescent reporters, or on expensive and time-consuming hydrogel-based approaches that requires specialized equipment. While aqueous-based clearing overcomes these challenges, there is a clear need for a method that is optimized for clearing musculoskeletal tissues and that can easily be implemented in a standard lab environment. Here, we present KneEZ Clear, a simple, rapid, and flexible aqueous-based method that renders mineralized and non-mineralized tissues of murine knee joints optically transparent. We show that KneEZ Clear, which is based on the EZ Clear method, is highly flexible, demonstrating efficacy in a wide range of murine musculoskeletal tissues including the vertebral column, hindlimb, skull, and teeth. Critically, KneEZ Clear does not require specialized equipment and retains endogenous signal from fluorophores and fluorescent proteins. Additionally, following clearing and wholemount imaging, precious samples can still be processed for subsequent 2D histological analyses for validation or further study. Finally, we show that KneEZ Clear can be applied to samples of disease models to reveal alterations in tissue architecture and homeostasis. The simplicity, versatility, and efficiency of KneEZ Clear for optical clearing of musculoskeletal tissues will accelerate our understanding of cellular interactions and dynamics in homeostasis and disease.