We experimentally study the effect of disorder on trapped quasi two-dimensional (2D) 87Rb clouds in the vicinity of the Berezinskii-Kosterlitz-Thouless (BKT) phase transition. The disorder correlation length is of the order of the Bose gas characteristic length scales (thermal de Broglie wavelength, healing length) and disorder thus modifies the physics at a microscopic level. We analyze the coherence properties of the cloud through measurements of the momentum distributions, for two disorder strengths, as a function of its degeneracy. For moderate disorder, the emergence of coherence remains steep but is shifted to a lower entropy. In contrast, for strong disorder, the growth of coherence is hindered. Our study is an experimental realization of the dirty boson problem in a well controlled atomic system suitable for quantitative analysis.