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The common approach to crystal-plasticity finite element modeling for load-bearing prediction of metallic structures involves the simulation of simplified grain morphology and substructure detail. This paper details a methodology for predicting the structure–property effect of as-manufactured microstructure, including true grain morphology and orientation, on cyclic plasticity, and fatigue crack initiation in biomedical-grade CoCr alloy. The methodology generates high-fidelity crystal-plasticity finite element models, by directly converting measured electron backscatter diffraction metal microstructure grain maps into finite element microstructural models, and thus captures essential grain definition for improved microstructure–property analyses. This electron backscatter diffraction-based method for crystal-plasticity finite element model generation is shown to give approximately 10% improved agreement for fatigue life prediction, compared with the more commonly used Voronoi tessellation method. However, the added microstructural detail available in electron backscatter diffraction–crystal-plasticity finite element did not significantly alter the bulk stress–strain response prediction, compared to Voronoi tessellation–crystal-plasticity finite element. The new electron backscatter diffraction-based method within a strain-gradient crystal-plasticity finite element model is also applied to predict measured grain size effects for cyclic plasticity and fatigue crack initiation, and shows the concentration of geometrically necessary dislocations around true grain boundaries, with smaller grain samples exhibiting higher overall geometrically necessary dislocations concentrations. In addition, minimum model sizes for Voronoi tessellation–crystal-plasticity finite element and electron backscatter diffraction–crystal-plasticity finite element models are proposed for cyclic hysteresis and fatigue crack initiation prediction.