Yacon presents prebiotic and hypoglycemic properties with a high fructan content. Pulsed vacuum osmotic dehydration (PVOD) is a process that can reduce water activity with small variations in nutritional properties. Yacon slices were dehydrated with two different solutions: fructose and sorbitol. The experiments were based on a central composite rotational design and the optimum condition set for the highest retention of fructans. The PVOD experiments were performed in 300 min, with vacuum pulse in the first 10 min. The independent variables were temperature (24–44 °C), vacuum pressure (49.4–200.6 mmHg) and osmotic solution concentration (22.0–60.8 °Brix). The dependent variables were fructan retention, weight reduction, water loss, solid gain, water activity and total color difference. The highest fructan retention was obtained with sorbitol, ranging from 28.13 to 82.03%, in contrast to the range of 2.79–39.48% obtained for the sample dehydrated with fructose. The optimum PVOD condition with sorbitol was concentration of 38 °Brix, temperature of 35 °C and vacuum pressure of 74 mmHg. For PVOD with fructose, the best results were obtained with a solution concentration of 35 °Brix, temperature between 24 and 30 °C and vacuum pulse above 100 mmHg.