A detailed characterization of the primary microstructure of laser-cladded NiCrAlY coatings deposited on two different substrate materials is presented in this article. Amdry 962 powder was used to deposit coatings by LENS (Laser Engineered Net Shaping) on Inconel 625 Ni-based superalloy and 316L stainless steel. An overall characterization of coatings was performed from a qualitative point of view with particular attention paid to cracks and pores. A description of microstructural aspects of the internal morphology of coatings, such as the microstructure, chemical, and phase composition were also investigated. The distribution of alloying elements, such as Fe, Mo, Nb, and Y, was investigated in cladded coatings on two different substrates. It was revealed that the cladded coatings contained cracks and gas voids typical for laser-cladding processes. The dendritic microstructure was the result of rapid solidification due to differences in the chemical composition of dendritic and interdendritic areas, which was related mainly to the yttrium concentration. Additionally, epitaxial growth during the initial stages of solidification was determined to be related to the diffusion of substrate alloying elements into the dilution zone. The strong influence of substrate materials, especially iron, in the final microstructure of coatings was analyzed. The oxidation of yttrium and the formation of Y-Al-O oxides were also analyzed.