Pectin, a complex polysaccharide found in plant cell walls, plays a crucial role in various industries due to its functional properties. The diluted alkali-soluble pectin (DASP) fractions that result from the stepwise extraction of apples and carrots were studied to evaluate their structural and rheological properties. Homogalacturonan and rhamnogalacturonan I, in different proportions, were the main pectin domains that composed DASP from both materials. Atomic force microscopy revealed that the molecules of apple DASP were longer and more branched. A persistence length greater than 40 nm indicated that the pectin molecules deposited on mica behaved as stiff molecules. The weight-averaged molar mass was similar for both samples. Intrinsic viscosity values of 194.91 mL·g−1 and 186.79 mL·g−1 were obtained for apple and carrot DASP, respectively. Rheological measurements showed greater structural strength for apple-extracted pectin, whereas carrot pectin was characterized by a higher linear viscoelasticity limit. This comparison showed that the pectin fractions extracted by diluted alkali are structurally different and have different rheological properties depending on their botanical origin. The acquired insights can enhance the customized use of pectin residue and support further investigations in industries relying on pectin applications.