We present a novel, three-stage method to solve the fluorescence lifetime imaging problem under low-photon conditions. In particular, we reconstruct the fluorophore concentration along with its support and fluorescence lifetime from the time-dependent measurements of scattered light exiting the domain. Because detectors used for these problems are photon counting devices, measurements are corrupted by Poisson noise. Consequently, we explicitly consider Poisson noise in conjunction with SPIRAL-$\ell_p$ -- a sparsity-promoting nonconvex optimization method -- to solve this problem. We demonstrate the effectiveness of the proposed three-stage method through numerical experiments in 2D fluorescence lifetime imaging.