The advent of X-ray free electron lasers is opening the soft X-ray spectral regime for investigation of ultrafast dynamics in isolated molecules. This spectral range allows for K-edge spectroscopy at the most abundant elements in organic molecules, C, N, and O. We are highlighting the opportunities for understanding excited state dynamics using site and element specificity, which are characteristics of core hole spectroscopy. Available spectroscopic schemes can be categorized into “direct” methods investigating the interaction between the X-ray photon and the molecule, and “indirect” methods focusing on the relaxation of the molecule via Auger processes. We review recent pioneering studies using “indirect” methods and point out future opportunities for studies employing “direct” methods.