Plant-based hydrocolloid systems which are mixed with different carbohydrate types are becoming popular due to vegan concerns for both non-food and food industry. In this study, different sugar types (d-allulose and sucrose) at different concentrations (20% and 40%) were used to explore their effects on the gelation and physical properties of agar–agar. For characterization of these agar–agar-based gel systems, in addition to common physical methods (moisture content, water activity, color, hardness, viscosity), novel methods such as TD-NMR relaxometry, and FTIR were also used to get deep insight of the microstructures and water dynamics of the gel systems. Results clearly indicated that sugar type and concentration were vital factors affecting the agar–agar gel properties and dynamics of the system. Utilization of allulose in the gel systems led to formation of less moist and softer agar–agar matrix characterized with longer T2 spin–spin relaxation times. This study will lead to designing new types of vegan agar–agar-based confectionery products such as soft candies that are considered as perfect composite gels.