The color expression of anthocyanins can be affected by a variety of environmental factors and structural characteristics. Anthocyanin acylation (type and number of acids) is known to be key, but the influence of acyl isomers (with unique stereochemistries) remains to be explored. The objective of this study was to investigate the effects of cis-trans configuration of the acylating group on the spectral and colorimetric properties of anthocyanins. Petunidin-3-rutinoside-5-glucoside (Pt-3-rut-5-glu) and Delphinidin-3-rutinoside-5-glucoside (Dp-3-rut-5-glu) and their cis and trans coumaroylated derivatives were isolated from black goji and eggplant, diluted in pH 1-9 buffers, and analyzed spectrophotometrically (380-700 nm) and colorimetrically (CIELAB) during 72 h of storage (25 °C, dark). The stereochemistry of the acylating group strongly impacted the spectra, color, and stability of the Dp and Pt anthocyanins. Cis acylated pigments exhibited the greatest λmax in all pH, as much as 66 nm greater than their trans counterparts, showing bluer hues. Cis acylation seemed to reduce hydration across pH, increasing color intensity, while trans acylation generally improved color retention over time. Dp-3-cis-p-cou-rut-5-glu exhibited blue hues even in pH 5 (C∗ab = 10, hab = 256°) where anthocyanins are typically colorless. Cis or trans double bond configurations of the acylating group affected anthocyanin spectral and stability properties.