D-Allulose (a monosaccharide and C3 epimer of fructose), one of the common rare sugars is getting attention due to its low caloric values. In this study, DAllulose was used as a replacement of sucrose at different ratios (D-Allulose/Sucrose: 35/0, 20/15, 10/25, 0/35) to formulate pectin-based soft confectionery gels. Soy protein isolate was also added to increase the protein content. Physical properties, such as hardness, moisture content, pH, and color, were measured for the gels. Higher hardness values were obtained for the soy protein containing gels due to pectin-soy protein interaction (p < 0.05). Also, higher moisture content was observed in soy protein containing gels (p < 0.05). In addition, nuclear magnetic resonance T-2 relaxation times were measured at low field (similar to 0.5 T) to determine how the water distribution in the samples changed and to observe how D-Allulose affected the polymer-water interactions. The study also showed that the presence of D-Allulose increased the crystallization tendency (% crystallinity of 7.9) of the pectin gels. X-ray diffraction results showed the D-allulose peaks at 33.76 and 48.68 degrees theta. Morphologies of the gels were also examined by scanning electron microscope. Sugar type and soy protein isolate addition were found to have significant impact on the gel formulations.