Abstract Both computational and experimental material discovery bring forth the challenge of exploring multidimensional and often non-differentiable parameter spaces, such as phase diagrams of Hamiltonians with multiple interactions, composition spaces of combinatorial libraries, processing spaces, and molecular embedding spaces. Often these systems are expensive or time-consuming to evaluate a single instance, and hence classical approaches based on exhaustive grid or random search are too data intensive. This resulted in strong interest towards active learning methods such as Bayesian optimization (BO) where the adaptive exploration occurs based on human learning (discovery) objective. However, classical BO is based on a predefined optimization target, and policies balancing exploration and exploitation are purely data driven. In practical settings, the domain expert can pose prior knowledge on the system in form of partially known physics laws and often varies exploration policies during the experiment. Here, we propose an interactive workflow building on multi-fidelity BO (MFBO), starting with classical (data-driven) MFBO, then expand to a proposed structured (physics-driven) sMFBO, and finally extending it to allow human in the loop interactive iMFBO workflows for adaptive and domain expert aligned exploration. These approaches are demonstrated over highly non-smooth multi-fidelity simulation data generated from an Ising model, considering spin-spin interaction as parameter space, lattice sizes as fidelity spaces, and the objective as maximizing heat capacity. Detailed analysis and comparison show the impact of physics knowledge injection and real time human decisions for improved exploration with increased alignment to ground truth.