We present a method to project time-bin qutrits stored in an echo-based quantum memory using several successive partial readouts of the memory. We demonstrate how this scheme can be used to implement projections onto a full set of mutually unbiased bases and, therefore, enables the characterization of arbitrary quantum states. Further, we study the integration of this protocol for the case of atomic frequency comb spin-wave storage by simulating the full storage process and performing a storage experiment with bright time-bin pulses in 151 Eu 3+ :Y2SiO5. In this context, a compound pulse for implementing partial readouts in quick succession is introduced and characterized.