The effect of spray drying on the different polyphenolic compounds present in the root of a purple-fleshed sweet potato variety of Ipomoea batatas native from Peru was performed by HPLC-QTOF-MSMS. Nine anthocyanins, including four peonidin, three cyanidin and two pelargonidin derivatives glycosylated with sophorose and/or glucose and acylated with caffeic, ferulic and p-hydroxybenzoic acid were identified. Twenty nine cinnamoylquinic acids (CiQA), including eight mono-CiQA, fourteen di-CiQA, and five tri-CiQA, were identified on the base of their MS fragmentation profile. Relevant amounts of feruloylquinic acid derivatives were identified. Among them, some di and tri-CiQAs containing feruloyl and caffeoyl moieties in their structures, and di-feruloylquinic acids were reported here, for the first time, in Ipomoea. Spray drying process negatively affected the different phenolic groups, with polyphenol losses representing around 90% of the initial amounts. Mono-CiQAs presenting feruloyl moieties and mono acylated peonidin derivatives with p-hydroxybenzoic acid were the less affected compounds.