Metal-organic frameworks (MOFs) are among the most promising materials for next-generation energy storage systems, including supercapacitors. Few studies, however, have examined the impact of particle morphology and degree of agglomeration on the energy storage performances of these materials. To address this, here we use coordination modulation to synthesise three samples of the conductive MOF Cu3(HHTP)2 (HHTP = 2,3,6,7,10,11-hexahydroxytriphenylene) with distinct microstructures. Evaluation of the performances of these samples in symmetric supercapacitors with organic and ionic liquid electrolytes demonstrated that samples with weakly agglomerated ‘flake-like’ particles, with short pores and many pore openings, display superior capacitive performances than samples with either weakly agglomerated ‘rod-like’ particle morphologies or strongly agglomerated ‘flake-like’ particles. The results of this study provide a target microstructure for conductive MOFs for energy storage applications.