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We have investigated the folding and assembly behavior of an alanine-based monomeric diamide and a cystine-based dimeric diamide bearing pyrene units and solubilizing alkyl chains at their C-termini andN-termini, respectively. In low-polarity solvents, the former molecule forms a folded 7-membered ring conformation with an intramolecular hydrogen bond, while the latter molecule forms a 14-membered ring through double intramolecular hydrogen bonds between two diamide units. Spectroscopic studies revealed that both folded states are thermodynamically unstable and eventually transform into more energetically stable supramolecular polymers. Importantly, compared to the alanine-based diamide, the cystine-based dimeric diamide exhibits a superior kinetic stability in the metastable folded state, as well asan increased thermodynamic stability in the aggregated state. Consequently, spontaneous transformation from the folded state into the aggregated state is retarded even under the conditions of rapid molecular diffusion. Accordingly, the initiation of supramolecular polymerization can be regulated via a seeding approach under microfluidic mixing conditions. Furthermore, the supramolecular polymer composed of the cystine-based dimeric diamide has a helical structure with an enhanced chiral excitonic coupling between the transition dipoles of the pyrene units. Taking advantage of the self-sorting behavior observed in a mixture of l-cysteine- and d-cysteine-based dimeric diamides, a two-step supramolecular polymerization from a racemic mixture was achieved by stepwise addition of the corresponding seeds.