Kanatzidis developed synthesis methodologies to synthesizing new chalcogenide materials and intermetallics. One of his notable contributions is the panoramic synthesis  method, which enables the design and discovery of novel materials. He is also credited with developing flux synthesis techniques that allow for reactions to occur at lower temperatures than conventional methods, leading to the formation of unique structures and compositions.
In addition to these contributions, Kanatzidis's research has resulted in the discovery of metal sulfide ion-exchangers, which have practical applications in the remediation of heavy metals in industrial waste water. These findings demonstrate his ability to not only generate new materials but also to identify and apply them in real-world settings.
Kanatzidis is also credited with defining the concept of nanostructuring in the thermoelectric field. By developing new approaches to controlling the structure and composition of thermoelectric materials at the nanoscale, he has contributed to the advancement of this field and the creation of high-performance materials with unique properties. These methods for achieving "nanostructuring" and all-scale architecturing of thermoelectric semiconductors, resulted in the creation of high-performance materials with unprecedented ZT figures of merit (ZT~2.5). These materials feature coherently embedded nanodots, such as those found in PbTe (a phenomenon known as endotaxy), which significantly reduce thermal conductivity by over 70%, while maintaining high electrical conductivity. This unique combination of properties allows for the attainment of very high ZT values exceeding 2.5 in nanostructured thermoelectric materials.
----Kanatzidis, along with fellow researcher Professor Robert P.H. Chang at Northwestern, developed a Novel solar cell technology that utilizes tin instead of lead perovskite. In their groundbreaking study, they published the first solid-state solar cell device incorporating a film of CsSnI3 perovskitein a solid-state dye-sensitized Gratzel cell, which achieved an efficiency of approximately 10%. Kanatzidis was also the first to demonstrate the functionality of CH3NH3SnI3-based solar cells, and he discovered the anomalous bandgap dependence between lead and tin-based solid solutions APb1-xSnxI3 (A=Cs, CH3NH3, formamidinium). This discovery revealed that bandgaps as low as 1.1 eV are achievable, which is useful in the development of tandem solar cells.
In 2016, Kanatzidis and Mohite demonstrated that 2D iodide perovskites form films with vertical slab orientation, and showed >12% efficiency in a solar cell with far better stability than corresponding 3D MAPbI3-based solar cells. . Since then, 2D iodide perovskites have become widely used in mixtures of 2D/3D perovskites for solar cells, exhibiting both high stability and efficiency.
In 2013 he reported the x-ray detecting properties of the perovskite CsPbBr semiconductor  with potential applications in gamma-ray spectroscopy having better than 1.4% energy resolution.
Kanatzidis has proposed ideas and concepts for predictive synthesis to new materials including "infinitely adaptive" homologous superseries and the panoramic synthesis strategy where with a single experiment all phases in the course of a given reaction can be detected. This offers a panoramic view of all the phases present, and could help unravel the mechanisms of how new materials form.
Kanatzidis is credited with inventing a new category of materials known as chalcogels. These unique inorganic compounds exhibit aerogel properties. Chalcogels have a sponge-like structure that enables them to effectively absorb heavy-metal atoms from polluted water. Due to their high surface area-to-volume ratio, even small pieces of chalcogels can purify thousands of liters of water. Chalcogels have demonstrated the ability to reduce mercury, lead, and cadmium concentrations to parts per trillion (ppt) levels as well as radionuclides. Biomimetic chalcogels containing bioinorganic FeS have been reported to photochemically convert  N to NH. The International Mineralogical Association named a new mineral, Kanatzidisite, belonging to the sulfosalt class with a composition of [BiSbS3][Te2].