An ideal quantum measurement collapses the wave function of a quantum system to an eigenstate of the measured observable, with the corresponding eigenvalue determining the measurement outcome. For a quantum non-demolition (QND) observable, i.e., one that commutes with the Hamiltonian generating the system's time evolution, repeated measurements yield the same result, corresponding to measurements with minimal disturbance. This concept applies universally to single quantum particles as well as to complex many-body systems. However, while QND measurements of systems with few degrees of freedom has been achieved in seminal quantum optics experiments, it is an open challenge to devise QND measurement of a complex many-body observable. Here, we describe how a QND measurement of the Hamiltonian of an interacting many-body system can be implemented in a trapped-ion analog quantum simulator. Through a single shot measurement, the many-body system is prepared in a narrow energy band of (highly excited) energy eigenstates, and potentially even a single eigenstate. Our QND scheme, which can be carried over to other platforms of quantum simulation, provides a novel framework to investigate experimentally fundamental aspects of equilibrium and non-equilibrium statistical physics including the eigenstate thermalization hypothesis (ETH) and quantum fluctuation relations.