One way to systematically control the microstructure of MOFs is using coordination modulation. Modulators, which have the same/similar chemical functionality as the organic linker molecule, influence the equilibrium governing the self-assembly process of MOFs by disrupting the formation of coordinative bonds between the linker molecules and the metal ions. Therefore, modulators help to regulate the rate of framework extension and particle growth, thus controlling the final morphology and degree of agglomeration of the formed particles. Varying the modulator is therefore an efficient way to systematically change the microstructure of MOFs, and can be used to obtain greater differences in microstructure than batch-to-batch variation alone. This method has been successfully employed in previous studies to determine the impact of particle morphology on the physical properties of other MOFs. Drawing on the above, this work uses coordination modulation to synthesise three samples of the layered conductive MOF Cu3(HHTP)2, (HHTP = 2,3,6,7,10,11-hexahydroxytriphenylene), each with distinctly different microstructures. This approach leads to greater differences in sample microstructure than previous work on this topic, with a variation in the length-to-width aspect ratio over the range of ca. 0.01 -37. Through this, we present a detailed study into the influence of microstructure on the capacitive performance of Cu3(HHTP)2 in symmetric supercapacitors with both organic and ionic liquid electrolytes. These studies conclusively showed that sample microstructure has a significant impact on the energy storage performances of layered MOFs. Samples with weakly agglomerated 'flake-like' particles, with very small length-to-width aspect ratios (< 1), performed best in MOF supercapacitors. These samples, with pore networks comprised of many short pores, displayed greater rate capabilities with organic electrolytes and significantly higher specific capacitances with ionic liquid electrolytes compared to samples with strongly agglomerated flake crystallites and weakly agglomerated 'rod-like' particles.