Abstract Although thousands of exoplanets have now been discovered, there is still a significant lack of observations of young planets only a few Myr old. Thus there is little direct evidence available to differentiate between various models of planet formation. The detection of planets of this age would provide much-needed data that could help constrain the planet formation process. To explore what transit observations of such planets may look like, we model the effects of large starspots and dust clouds on the depths of exoplanet transits across multiple wavelengths. We apply this model to the candidate planet PTFO 8-8695b, whose depths vary significantly across optical and infrared wavelengths. Our model shows that, while large starspots can significantly increase the color dependence of planetary transits, a combination of starspots and a large cloud surrounding the planet is required to reproduce the observed transit depths across four wavelengths.