In the present study, Inconel 686 thick-wall part manufactured utilizing gas metal arc welding-based wire arc directed energy deposition (WA-DED) was examined. The microstructure and mechanical properties of the fabricated Inconel 686 component across different sections, such as bottom, middle, and top, were explored, and the influence of cryogenic treatments, such as shallow and deep, on the properties of the fabricated specimens was examined. The optical and scanning electron microscopy revealed differences in microstructure across various regions of the deposited metal. The bottom region showed a columnar structure, the intermediate region displayed a combination of cellular structures, and the top layer featured an equiaxed structure. These variations contribute to heterogeneity and anisotropy in the mechanical characteristics. Moreover, the microstructure of the deep cryogenic treatment (DCT)-treated samples exhibited a finer grain structure in contrast to both the as-built and shallow cryogenic treatment (SCT)-treated WA-DED samples attributed to grain refinement. X-ray diffraction analysis observed that applying DCT decreased grain size, with the average grain size of the DCT-treated sample measuring 22.81 nm, while concurrently increasing the dislocation density to 19.22 × 10–4 nm–2. Energy-dispersive X-ray spectroscopy point analysis, elemental mapping, and line mapping were conducted to study the microsegregation and spatial distribution of alloying elements in the grain boundaries and interdendritic regions. Results indicated intensified segregation tendencies of alloying elements molybdenum (Mo) and tungsten (W) with increasing deposited height, peaking in the lowermost region. However, DCT samples exhibit reduced elemental segregation compared to as-built and SCT samples. The tensile strength and microhardness showed substantial differences across various areas. Cryogenic treatments considerably improved the mechanical properties of WA-DED specimens compared to their as-built state. As a result, the tensile strength improved by 7.23%, and the hardness strength increased by 8.98%.