The effect of carbon dioxide-argon radio frequency cold plasma treatment on the in vitro digestion and structural characteristics of granular and non-granular waxy maize, potato, and rice starches was investigated in this study. The effect on the fine structure of waxy potato was very minimal after plasma treatment irrespective of their granular or non-granular form. The short chain length (SCL) of waxy maize and rice (granular and non-granular) starches was reduced leading to subsequent increases in the long chain length (LCL). In vitro digestibility studies showed that cold plasma treatment enhanced (p < 0.05) the amount of slowly digestible starches (5.62%; 10.24%) and resistant starches (0.28%; 85.66%) in non-granular waxy maize (WMS NG) and granular waxy potato starches (WPS G), respectively. The amount of rapidly digestible starches increased in granular waxy maize starch (WMS G) (85.08%) but was unaffected in non-granular waxy rice (WRS NG), WPS G, and non-granular waxy potato starches after plasma treatment. FTIR-ATR data confirmed the ability of cold plasma to induce cross-linking in waxy starches specifically in WMS NG, WRS G, WRS NG, and WPS G. Overall, the unit and internal chain structure of the waxy starches were mostly unaffected by radio frequency plasma treatment. Cross-linking served as the dominant mechanism by which plasma altered the structure and digestibility of these starches. PRACTICAL APPLICATION: Cold plasma technology has been suggested as a green technique for starch modification. More research is, however, needed to facilitate the industrial scale up of this technology. In this study, we utilized a carbon dioxide-argon radio frequency cold plasma to modify waxy maize, rice and potato starches. Cold plasma treatment resulted in starches that were resistant to digestion and were highly cross-linked. The cross-linking would give the starches the ability to possibly withstand the high temperatures and shear that can be applied during industrial processing.