We present an experimental study identifying structural reasons that degrade spin-polarization of Co2MnSi thin films deposited on MgO(001) substrates. Through the fabrication of magnetic tunnel junctions, we measure a range of values for tunneling magneto-resistance (TMR) ratios following post-deposition annealing and epitaxial crystallization of the Heusler film. These TMR ratios reflect qualitatively the change in spin polarization of the Co2MnSi thin films. Low-temperature annealing results in low spin-polarization due to a high fraction of an amorphous phase. As annealing temperatures increase, the fraction of L21 and B2 chemically ordered phases increases, thus improving significantly the spin-polarization. However, for samples annealed at higher temperatures, significant degradation in the cubic magneto-crystalline anisotropy is observed, which we attribute to the detection of manganese diffusion into the MgO substrate. This Mn diffusion is manifested in a reduction of the value of the TMR ratio, namely, the spin polarization. Additionally, the maximum TMR ratio measured here, approximately 65% at room-temperature, is limited because the semi-coherent interface of Co2MnSi with the MgO substrate terminates with a Mn-Si layer.