Trapped atoms and ions, which are among the best-controlled quantum systems, find widespread applications in quantum science. For molecules, a similar degree of control is currently lacking owing to their complex energy-level structure. Quantum-logic protocols in which atomic ions serve as probes for molecular ions are a promising route for achieving this level of control, especially for homonuclear species that decouple from blackbody radiation. Here, a quantum-nondemolition protocol on single trapped N-2(+) molecules is demonstrated. The spin-rovibronic state of the molecule is detected with >99% fidelity, and a spectroscopic transition is measured without destroying the quantum state. This method lays the foundations for new approaches to molecular spectroscopy, state-to-state chemistry, and the implementation of molecular qubits.