We present a novel architecture for learning geometry-aware preconditioners for linear partial differential equations (PDEs). We show that a deep operator network (Deeponet) can be trained on a simple geometry and remain a robust preconditioner for problems defined by different geometries without further fine-tuning or additional data mining. We demonstrate our method for the Helmholtz equation, which is used to solve problems in electromagnetics and acoustics; the Helmholtz equation is not positive definite, and with absorbing boundary conditions, it is not symmetric.