In fluorescence diffuse optical tomography (fDOT), the accuracy of reconstructed fluorescence distributions highly depends on the knowledge of the tissue optical heterogeneities for correct modeling of light propagation. Common approaches are to assume homogeneous optical properties or, when structural information is available, assign optical properties to various segmented organs, which is likely to result in inaccurate reconstructions. Furthermore, DOT based only on intensity (continuous wave-DOT) is a nonunique inverse problem, and hence, cannot be used to retrieve simultaneously maps of absorption and diffusion coefficients. We propose a method that reconstructs a single parameter from the excitation measurements, which is used in the fDOT problem to accurately recover fluorescence distribution.