The detailed characterization of non-trivial coherence properties of composite quantum systems of increasing size is an indispensable prerequisite for scalable quantum computation, as well as for understanding non-equilibrium many-body physics. Here, we show how autocorrelation functions in an interacting system of phonons as well as the quantum discord between distinct degrees of freedoms can be extracted from a small controllable part of the system. As a benchmark, we show this in chains of up to 42 trapped ions, by tracing a single phonon excitation through interferometric measurements of only a single ion in the chain. We observe the spreading and partial refocusing of the excitation in the chain, even on a background of thermal excitations. We further show how this local observable reflects the dynamical evolution of quantum discord between the electronic state and the vibrational degrees of freedom of the probe ion.