Protein isolation and purification are critical steps in protein research involving recombinant DNA technology. Numerous techniques have been developed to optimize these processes for efficiency. Escherichia coli is the most common expression host for recombinant protein production; however, low expression levels or solubility often pose challenges for subsequent steps. To address this issue, target proteins are frequently linked with large tags, such as maltose binding protein (MBP). In this study, we present two examples of improved characteristics observed after incorporating MBP into target proteins. However, during the crystallization process, the MBP tag undergoes unexpected autocleavage in many forms of MBP fusion protein crystals. Our study highlights MBP as a beneficial tag for enhancing protein characteristics, though careful engineering of the linker sequence is necessary for selective cleavage of MBP fusion proteins.