The structure of polydiacetylene (PDA) supramolecules offers carboxylic acid-terminated alkyl side-chains around a π conjugated polymer backbone. Exposure of these supramolecules to alkylamines induced disruption of the conjugated PDA backbone via intercalation as revealed by a colorimetric/ fluorometric response. This response is demonstrated to be dependent on the length of the alkylamine, offering a new view on intercalation in PDA systems with respect to supramolecules. It is found that this critical carbon chain length of alkylamine required to induce a colour change response must be greater than the alkyl side-chain length of PDA in order to interact with the conjugated backbone. Intercalation of longer species is also found to induce supramolecule aggregation resulting in destabilised PDA suspensions.