We propose a new reconstruction algorithm for fluorescence diffuse optical tomography, which is designed for highly heterogeneous objects, such as biological tissues. It is a two-step algorithm that exploits continuous-wave measurements acquired at both excitation and fluorescence wavelengths. First, an optical inhomogeneity map, which depends on both absorption and diffusion coefficients, is obtained from excitation measurements. Second, the fluorescence distribution is reconstructed considering the recovered optical inhomogeneity map. The algorithm includes dimensionality reduction techniques, namely measurement compression and structured illumination, which significantly reduce acquisition and reconstruction times. The algorithm has been tested on experimental data acquired from tissuemimicking phantoms considering sparsity priors. We demonstrate the feasibility and effectiveness of this new approach that allows the fluorescence reconstruction quality to be improved with respect to that provided by the standard normalized Born method.