In this study, the microstructure of polycrystalline Co-doped BaFe2As2 superconducting bulks was comprehensively analyzed. The synthesis process involved ball milling and subsequent spark plasma sintering (SPS). A strong correlation between the microstructure and synthesis conditions was observed. Specifically, when mechanochemical synthesis of raw metal powders was carried out at a ball milling energy (EBM) of 100 MJ/kg, the resulting Co-BaFe2As2 bulk contained nanograins with a high density of planar defects and exhibited a high critical current density (Jc) under both magnetic and self-fields. The findings suggest that planar defects are one of the influential factors on the superconducting properties. Atomic-resolution microstructural characterization revealed that the planar defects are parallel to (001) and exhibit distinctive atomic arrangements. Atomic-resolution elemental mappings displayed a remarkable barium concentration in planar defects and grain boundaries compared to the BaFe2As2 matrix. Local strain fields were also observed around planar defects, especially near their edges. These nanoscale strain fields could be considered as volumetric pinning centers, and effectively pin flux vortices in the random crystal orientation, thereby increasing Jc in the Fe-based superconducting bulk. Additionally, an extended investigation was performed to include a K-doped BaFe2As2 bulk that exhibits similar planar defects. Based on the results of the microstructural analysis, speculations were mode on the evolution process of the microstructure during the preparation of BaFe2As2 bulks.