The micro-mechanical properties of complex biomaterials play an important role in tissue engineering and regenerative medicine, by regulating cellular processes and signalling. Local characterization of complex tissues while immersed in liquids proves to be very difficult to perform. We therefore present a method to derive viscoelastic micro-mechanical properties via non-destructive nano-indentation measurements in liquid. This technique is featured with a fiber-optical ferrule-top micro-machined force transducer, enabling a wide range of mechanical tests: from quasi-static experiments to derive elastic moduli, to step-response tests (e.g. creep, stress-relaxation), dynamic mechanical analysis (DMA) and constant strain rate tests to characterize sample viscoelastic behaviour. As a complex application we here present the osteochondral (OC) interface, which gradually ranges from hard and stiff bone regions towards softer and viscoelastic articular cartilage covering joint surface. The osteochondral plugs were collected from medial femoral condyle of cadaveric knees and measured at 37°C to mimic in-vivo physiological-like conditions. The stiffness of articular cartilage was 1.58±0.06 MPa, whereas subchondral bone plate could be categorized in “softer” region with 68.24±37.43 MPa, and a “stiffer” region with 683.68±622.88 MPa. The high stiffness in the “hard” region could be attributed to the mineralized matrix in the contact area, whereas the contribution of gel-like material, containing cell processes, along with osteocytes was larger in the “soft” region of the subchondral bone plate, leading to lower stiffness. These results might correlate with differences in extracellular matrix (ECM) composition and micro-architecture and are essential for engineering functional gradient scaffolds to better understand cell-ECM interactions.