Joint mixed modeling is an attractive approach for the analysis of a scalar response measured at a primary endpoint and longitudinal measurements on a covariate. In the standard Bayesian analysis of these models, measurement error variance and the variance/covariance of random effects are a priori modeled independently. The key point is that these variances cannot be assumed independent given the total variation in a response. This article presents a joint Bayesian analysis in which these variance terms are a priori modeled jointly. Simulations illustrate that analysis with multivariate variance prior in general lead to reduced bias (smaller relative bias) and improved efficiency (smaller interquartile range) in the posterior inference compared with the analysis with independent variance priors.