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Elemental type-II superconducting niobium is the material of choice for superconducting radiofrequency cavities used in modern particle accelerators, light sources, detectors, sensors, and quantum computing architecture. An essential challenge to increasing energy efficiency in rf applications is the power dissipation due to residual magnetic field that is trapped during the cool down process due to incomplete magnetic field expulsion. New SRF cavity processing recipes that use surface doping techniques have significantly increased their cryogenic efficiency. However, the performance of SRF Nb accelerators still shows vulnerability to a trapped magnetic field. In this manuscript, we report the observation of a direct link between flux trapping and incomplete flux expulsion with spatial variations in microstructure within the niobium. Fine-grain recrystallized microstructure with an average grain size of 10–50 µm leads to flux trapping even with a lack of dislocation structures in grain interiors. Larger grain sizes beyond 100–400 µm do not lead to preferential flux trapping, as observed directly by magneto-optical imaging. While local magnetic flux variations imaged by magneto-optics provide clarity on a microstructure level, bulk variations are also indicated by variations in pinning force curves with sequential heat treatment studies. The key results indicate that complete control of the niobium microstructure will help produce higher performance superconducting resonators with reduced rf losses¹related to the magnetic flux trapping.