Sweetpotato [Ipomoea batatas (L.) Lam.], a food crop with both nutritional and medicinal uses, plays essential roles in food security and health-promoting. Chlorogenic acid (CGA), a polyphenol displaying several bioactivities, is distributed in all edible parts of sweetpotato. However, little is known about the specific metabolism of CGA in sweetpotato. In this study, IbPAL1, which encodes an endoplasmic reticulum-localized phenylalanine ammonia lyase (PAL), was isolated and characterized in sweetpotato. CGA accumulation was positively associated with the expression pattern of IbPAL1 in a tissue-specific manner, as further demonstrated by overexpression of IbPAL1. Overexpression of IbPAL1 promoted CGA accumulation and biosynthetic pathway genes expression in leaves, stimulated secondary xylem cell expansion in stems, and inhibited storage root formation. Our results support a potential role for IbPAL1 in sweetpotato CGA biosynthesis and establish a theoretical foundation for detailed mechanism research and nutrient improvement in sweetpotato breeding programs.