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Abstract Immersed boundary methods are high-order accurate computational tools used to model geometrically complex problems in computational mechanics. While traditional finite element methods require the construction of high-quality boundary-fitted meshes, immersed boundary methods instead embed the computational domain in a structured background grid. Interpolation-based immersed boundary methods augment existing finite element software to non-invasively implement immersed boundary capabilities through extraction. Extraction interpolates the structured background basis as a linear combination of Lagrange polynomials defined on a foreground mesh, creating an interpolated basis that can be easily integrated by existing methods. This work extends the interpolation-based immersed isogeometric method to multi-material and multi-physics problems. Beginning from level-set descriptions of domain geometries, Heaviside enrichment is implemented to accommodate discontinuities in state variable fields across material interfaces. Adaptive refinement with truncated hierarchically refined B-splines (THB-splines) is used to both improve interface geometry representations and to resolve large solution gradients near interfaces. Multi-physics problems typically involve coupled fields where each field has unique discretization requirements. This work presents a novel discretization method for coupled problems through the application of extraction, using a single foreground mesh for all fields. Numerical examples illustrate optimal convergence rates for this method in both 2D and 3D, for partial differential equations representing heat conduction, linear elasticity, and a coupled thermo-mechanical problem. The utility of this method is demonstrated through image-based analysis of a composite sample, where in addition to circumventing typical meshing difficulties, this method reduces the required degrees of freedom when compared to classical boundary-fitted finite element methods.