This data set contains the absorption spectra of poly(3-hexylthiophene): 1-(3-methoxy-carbonyl)propyl-1-phenyl-(6,6)C61 (P3HT:PCBM) solar cells from which the thickness of the photoactive layer has been measured with spatial resolution. The spectra are documented in the Full-Metadata Format (Riede et al. 2010, doi:10.1016/j.cpc.2009.11.014). The experiment and the data analysis algorithm are described in Sylvester-Hvid et al.: Non-destructive lateral mapping of the thickness of the photoactive layer in polymer based solar cells (accepted for publication in Progress of Photovoltaics).