The use of multidimensional entanglement opens new perspectives for quantum information processing. However, an important challenge in practice is to certify and characterize multidimensional entanglement from measurement data that are typically limited. Here, we report the certification and quantification of two-photon multidimensional energy-time entanglement between many temporal modes, after one photon has been stored in a crystal. We develop a method for entanglement quantification which makes use of only sparse data obtained with limited resources. This allows us to efficiently certify an entanglement of formation of 1.18 ebits after performing quantum storage. The theoretical methods we develop can be readily extended to a wide range of experimental platforms, while our experimental results demonstrate the suitability of energy-time multidimensional entanglement for a quantum repeater architecture.