Potatoes are an important food crop that undergo postharvest storage, reconditioning, and cooking. Colored-flesh varieties of potatoes are rich in phenolic acids and anthocyanins. Previous studies have suggested that purple-flesh potatoes can inhibit colon cancer cells in vitro and reduce colon carcinogenesis in vivo. Vacuum frying (VF), as an alternative to conventional frying (CF), reduces fat content and may promote polyphenol retention in potato chips. We examined the impacts of reconditioning (storing at 13 • C for 3 weeks following the 90-day cold storage at 7 • C) and frying method on phenolic chemistry and in vitro colon cancer stem cell (CCSC) inhibitory activity of purple-flesh potato chips. We found that reconditioned chips exhibited higher total phenolic content (TPC) than nonreconditioned chips. We found that VF chips had lower TPC than CF chips. We observed no interaction between treatments. We found that VF chips had 27% higher total monomeric anthocyanin levels than CF chips, and observed a significant interaction between treatments. We found that VF chips had higher concentrations of caffeic acid (42%-72% higher), malvidin (46%-98% higher), and pelargonidin (55%-300% higher) than CF chips. We found that reconditioning had no effect. We found that VF chips had greater in vitro CCSC inhibitory activity than CF chips. Our results suggest that VF can improve the phytochemical profile and health-related functionality of purple-flesh potato chips, but additional studies are needed to determine if these results translate to the in vivo situation.