Type of sugar and gelling agents used in confectionery formulations have vital importance since they directly influence physicochemical properties during storage. In this study, the effect of a non-caloric rare sugar, D-allulose (formerly called D-psicose) on the starch based confectionery gels were investigated in the presence and absence of soy protein isolate (SPI) using different experimental techniques for 28 days. For characterization of the formulized gel systems, common techniques were used (SEM, DSC, XRD, moisture content, water activity, hardness and color). Time Domain Nuclear Magnetic Resonance (TD-NMR) technique was also employed to explain dynamics in the systems. Sugar type was found to be a very significant factor affecting gel characteristics and retrogradation. Results showed that D-allulose containing formulations were less prone to retrogradation and showed smaller changes upon storage by supporting presence of better gel network. According to X-ray results, sucrose containing formulations were more susceptible to crystallization. T-2 relaxation spectra obtained from NMR experiments showed that number of distinct peaks reduced with the addition of SPI while relaxation times of peaks changed when different type of sugar.