The influence of combined shear stress and oscillating hydrostatic pressure (OHP), two forms of physical forces experienced by articular cartilage (AC) in vivo, on chondrogenesis, is investigated in a unique bioreactor system. Our system introduces a single reaction chamber design that does not require transfer of constructs after seeding to a second chamber for applying the mechanical forces, and, as such, biochemical and mechanical stimuli can be applied in combination. The biochemical and mechanical properties of bovine articular chondrocytes encapsulated in agarose scaffolds cultured in our bioreactors for 21 days are compared to cells statically cultured in agarose scaffolds in addition to static micromass and pellet cultures. Our findings indicate that glycosaminoglycan and collagen secretions were enhanced by at least 1.6-fold with scaffold encapsulation, 5.9-fold when adding 0.02 Pa of shear stress and 7.6-fold with simultaneous addition of 4 MPa of OHP when compared to micromass samples. Furthermore, shear stress and OHP have chondroprotective effects as evidenced by lower mRNA expression of β1 integrin and collagen X to non-detectable levels and an absence of collagen I upregulation as observed in micromass controls. These collective results are further supported by better mechanical properties as indicated by 1.6–19.8-fold increases in elastic moduli measured by atomic force microscopy.