The cell structure of fruits and vegetables is changed due to freezing. The application of these changes by prefreezing for improving the physical quality of baked sweet potatoes was investigated here. The cell structures and physical properties were analyzed focusing on bio-electrochemical impedance spectroscopy (BIS), X-ray computed tomography (X-ray CT), increasing sample temperature, and mechanical properties. The BIS indicated that the cell membranes were destroyed by both freezing and baking. The X-ray CT images showed that the frozen-baked sample could be maintained more inside the tissue area than the raw-baked sample: this indicated that prefreezing significantly inhibited shrinkage during baking. Moreover, the freezing treatments significantly reduced the temperature increase during baking, maximum penetration stress, and elastic modulus of their tissues, which could be attributed to ice crystallization. This study suggests that prefreezing may be effective for the storage, control, or improvement in physical quality of baked sweet potatoes.