A multivariate positive definite estimator of the covariance matrix of noisy and asynchronously observed asset returns is proposed. We adopt a Bayesian Dynamic Linear Model which allows us to interprete microstructure noise as measurement errors, and the asynchronous trading as missing observations in an otherwise synchronous series. These missing observations are treated as any other parameter of the problem as typically done in a Bayesian framework. We use an augmented Gibbs algorithm and thus sample the covariance matrix, the observational error variance matrix, the latent process and the missing observations of the noisy process from their full conditional distributions. Convergence issues and robustness of the Gibbs sampler are discussed. A simulation study compares our Bayesian estimator with recently proposed pair-wise QMLE-type and Multivariate Realized Kernel estimators, under different liquidity and microstructure noise conditions. The results suggest that our estimator is superior in terms of RMSE in both a two-and ten-dimensional settings, especially with dispersed and high missing percentages and with high noise. This suggests that our Bayesian estimator is more robust in severe conditions, such as portfolios of assets with heterogeneous liquidity profiles, or particularly illiquid, or when there is a high level of microstructure noise in the market.