We consider the problem of extracting features from individual sources in a multisource audio recording using a general source separation algorithm. The main issue is to estimate and propagate the uncertainty over the separated source signals, so as to robustly estimate the features despite source separation errors. While state-of-the-art techniques estimate the uncertainty in a heuristic manner, we propose to integrate over the parameter space of the source separation algorithm. We apply variational Bayes to estimate the posterior probability of the sources and subsequently derive the expectation of the features by moment matching. Experiments over stereo mixtures of three or four sources show that the proposed method provides the best results in terms of the root mean square (RMS) error on the estimated features.