Space-based photometric transit searches, such as the ESA mission Eddington (planned for launch in 2007), are expected to detect large numbers of terrestrial planets outside the solar system, including some Earth-like planets. Combining simplicity of concept with efficiency, the transit method consists in detecting the periodic luminosity drop in stellar light curves caused by the transit of a planet in front of its parent star. In a previous paper (Aigrain & Favata [CITE], hereafter Paper I), we developed a Bayesian transit detection algorithm and evaluated its performance on simulated light curves dominated by photon noise. In this paper, we examine the impact of intrinsic stellar variability. Running the algorithm on light cur...