Native potato starch has a semi-crystalline structure associated with a low glycemic index. Microwave vacuum drying (MWVD) produces crispy snacks under mild temperatures, reducing starch structural changes. However, blanching pretreatment gelatinizes starch, reducing crystallinity. A promising alternative is drying raw or blanched-then-cooled potatoes by MWVD. Cooling the blanched potato before MWVD aims to promote the partial return of the crystalline structure. Thus, this study evaluated how different pretreatments affect potato chips’ starch structure and physical properties. Three samples were dried by MWVD: (i) raw (MWVD-RW), (ii) blanched (MWVD-BL), and (iii) blanched followed by cooling (4 °C for 48 h) (MWVD-BLC) potatoes. MWVD-RW samples presented a higher starch crystallinity (16.9%), which disappeared in MWVD-BL samples and partially returned in MWVD-BLC (8.7%). MWVD-BL and MWVD-BLC samples presented lower bulk (<0.338 g cm−3) density and higher porosity (>74%) and crispness. On the other hand, MWVD-BLC samples presented intermediate characteristics for color, true density, and porous distribution compared to others. All samples showed high porosity (>69%) and crispy texture. Therefore, based on the quality assessment, the MWVD-RW and MWVD-BLC produced healthy and crispy oil-free chips with a potentially lower glycemic index.