Sequential metabolic enzymes can form supramolecular complexes named metabolons in vivo through enzyme-enzyme association or aggregation to facilitate efficient substrate channeling. By separately labeling enzymes with lysine-targeting carboxylic acid succinimidyl ester fluorophores of distinct excitation wavelengths, this research presents a quantitative study of polymer-entrapment-induced in vitro multi-enzyme aggregation from three Krebs cycle enzymes using Forster resonance energy transfer (FRET) to find potential polymer materials for immobilizing enzyme cascades and inducing the metabolon biomimic formation on electrodes. The effect of hydrophobic modification of linear polyethylenimine, Nafion, and chitosan polymers on metabolon formation has been investigated through photobleaching FRET imaging in addition to traditional steady-state fluorescence spectroscopy. By partially destroying FRET acceptors of longer excitation wavelength, increased fluorescence from dequenched donors of shorter excitation wavelength was measured and enzyme interactions in terms of energy-transfer efficiencies were mapped point by point. Results show that trimethyloctadecylammonium-modified Nafion works best in inducing multi-enzyme aggregation and exhibits a promising future in immobilized metabolon biomimics with the most uniform enzyme organization, as indicated by the protein distance distribution.