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The use of bacterial production could improve commercial feasibility for biochemicals such as pharmaceuticals and natural products. However, many non-native reactions in bacterial hosts have unacceptably low yields due to pathway toxicity or competition with other cellular processes. Compartmentalization is a potential solution to these problems, but compartmentalized organelles were long thought to be found only in eukaryotic cells. Remarkably, bacterial microcompartments (MCPs) are protein-based organelles that perform this sequestration function. We aim to apply these MCPs for metabolic engineering and the enhancement of biosynthesis pathways that do not function optimally in the cytosol. MCPs may also serve as a scaffold for application outside of the cell.To achieve this goal, we characterized the stability of MCPs when exposed to a range of pH and temperature to define the limitations of this complex structure. We next demonstrated that it is possible to form chimeric MCPs by combining shell proteins from different systems in nature. Importantly, we found that these changes to shell protein structure can enhance the function of the encapsulated pathway. We discovered that pathway performance can also be improved by a single point mutation to the pore of a shell protein, likely altering small molecule diffusion across the shell. We are investigating the role of shell protein pore chemistry in tuning small molecule diffusion. Finally, we test signal sequence peptides at the C-terminus of proteins and find that variation of signal peptide sequence results in altered expression level and loading within MCPs. In total, these tools improve our ability to design custom bacterial organelles to control the partitioning of chemical reactions within cells.