Matrix factorization (MF) has been widely applied to collaborative filtering in recommendation systems. Its Bayesian variants can derive posterior distributions of user and item embeddings, and are more robust to sparse ratings. However, the Bayesian methods are restricted by their update rules for the posterior parameters due to the conjugacy of the priors and the likelihood. Neural networks can potentially address this issue by capturing complex mappings between the posterior parameters and the data. In this paper, we propose a variational auto-encoder based Bayesian MF framework. It leverages not only the data but also the information from the embeddings to approximate their joint posterior distribution. The approximation is an iterative procedure with cross feedback of user and item embeddings to the others' encoders. More specifically, user embeddings sampled in the previous iteration, alongside their ratings, are fed back into the item-side encoders to compute the posterior parameters for the item embeddings in the current iteration, and vice versa. The decoder network then reconstructs the data using the MF with the currently re-sampled user and item embeddings. We show the effectiveness of our framework in terms of reconstruction errors across five real-world datasets. We also perform ablation studies to illustrate the importance of the cross feedback component of our framework in lowering the reconstruction errors and accelerating the convergence.