Non-destructive detection of photonic qubits is an enabling technology for quantum information processing and quantum communication. For practical applications such as quantum repeaters and networks, it is desirable to implement such detection in a way that allows some form of multiplexing as well as easy integration with other components such as solid-state quantum memories. Here we propose an approach to non-destructive photonic qubit detection that promises to have all the mentioned features. Mediated by an impurity-doped crystal, a signal photon in an arbitrary time-bin qubit state modulates the phase of an intense probe pulse that is stored during the interaction. Using a thulium-doped waveguide in lithium niobate, we perform a proof-of-principle experiment with macroscopic signal pulses, demonstrating the expected cross-phase modulation as well as the ability to preserve the coherence between temporal modes. Our findings open the path to a new key component of quantum photonics based on rare-earth-ion doped crystals.