Long-duration quantum memories for photonic qubits are essential components for achieving long-distance quantum networks and repeaters. The mapping of optical states onto coherent spin-waves in rare earth ensembles is a particularly promising approach to quantum storage. However, it remains challenging to achieve long-duration storage at the quantum level due to read-out noise caused by the required spin-wave manipulation. In this work, we apply dynamical decoupling techniques and a small magnetic field to achieve the storage of six temporal modes for 20, 50, and 100 ms in a ¹⁵¹ Eu ³⁺ :Y ₂ SiO ₅ crystal, based on an atomic frequency comb memory, where each temporal mode contains around one photon on average. The quantum coherence of the memory is verified by storing two time-bin qubits for 20 ms, with an average memory output fidelity of F  = (85 ± 2)% for an average number of photons per qubit of μ _in  = 0.92 ± 0.04. The qubit analysis is done at the read-out of the memory, using a type of composite adiabatic read-out pulse we developed.