In this paper we present a PDE solution framework for high-order discretizations of conjugate heat transfer (CHT) problems on non-body-conforming meshes. The framework consists of a discontinuous Galerkin (DG) discretization, a simplex cut-cell technique, and an anisotropic output-based adaptive scheme. With the cut-cell technique, the mesh generation process is completely decoupled from the interface definitions. In addition, the adaptive scheme combined with the DG discretization automatically adjusts the mesh in each sub-domain and achieves high-order accuracy in outputs of interest, namely heat flux across an interface. We demonstrate our proposed framework through several multi-domained CHT problems consisting of laminar and turbulent flows, curved geometry, and highly coupled heat transfer regions. The combination of these attributes yield nonintuitive coupled interactions between fluid and solid domains, which can be di cult to capture with user generated meshes. Our proposed automatic mesh generation and adaptation scheme o↵ers a hands-free capability allowing for streamlined solutions and physical insight to complex CHT problems.