Lyophilization of proteins can introduce lot-to-lot variabilities in different product properties that are crucial in terms of product performance and stability. As these variations can raise several issues related to product quality, the characterization of the physical and chemical properties of protein lots is necessary, to identify critical deviations between the lots and to rationally control the process to yield an acceptable product. The critical concerns are potential quality issues of the drug product and (negative) effects on the reconstitution behavior of the solid-state lyophilized proteins. This review provides an overview of powder properties and physicochemical attributes of solid protein formulations manufactured by lyophilization that are potentially associated with lot-to-lot variabilities. Brief descriptions of various conventional, as well as novel, analytical techniques, which are suitable for characterizing the properties of the pharmaceutical protein powder, are discussed.