Starch-based isomalto/malto-polysaccharides (IMMPs) are soluble dietary fibres produced by the incubation of α-(1 → 4) linked glucans with the 4,6-α-glucanotransferase (GTFB) enzyme. In this study, we investigated the reaction dynamics of the GTFB enzyme by using isoamylase debranched starches as simplified linear substrates. Modification of α-glucans by GTFB was investigated over time and analysed with 1H NMR, HPSEC, HPAEC combined with glucose release measurements. We demonstrate that GTFB modification of linear substrates followed a substrate/acceptor model, in which α-(1 → 4) linked glucans DP ≥ 6 functioned as donor substrate, and α-(1 → 4) linked malto-oligomers DP < 6 functioned as acceptor. The presence of α-(1 → 4) linked malto-oligomers DP < 6 resulted in higher GTFB transferase activity, while their absence resulted in higher GTFB hydrolytic activity. The information obtained in this study provides a better insight into GTFB reaction dynamics and will be useful for α-glucan selection for the targeted synthesis of IMMPs in the future.