A promising approach for multi-qubit quantum registers is to use optically addressable spins to control multiple dark electron-spin defects in the environment. While recent experiments have observed signatures of coherent interactions with such dark spins, it is an open challenge to realize the individual control required for quantum information processing. Here, we demonstrate the heralded initialisation, control and entanglement of individual dark spins associated to multiple P1 centers, which are part of a spin bath surrounding a nitrogen-vacancy center in diamond. We realize projective measurements to prepare the multiple degrees of freedom of P1 centers—their Jahn-Teller axis, nuclear spin and charge state—and exploit these to selectively access multiple P1s in the bath. We develop control and single-shot readout of the nuclear and electron spin, and use this to demonstrate an entangled state of two P1 centers. These results provide a proof-of-principle towards using dark electron-nuclear spin defects as qubits for quantum sensing, computation and networks.