Pyranoanthocyanins are vibrant, naturally derived pigments formed by the reaction of an anthocyanin with a cofactor containing a partially negatively charged carbon. This study compared the thermal stability and degradation products of 10-carboxy-pyranocyanidin-3-glucoside (pyruvic acid cofactor), 10-methyl-pyranocyanidin-3-glucoside (acetone cofactor), and 10-catechyl-pyranocyanidin-3-glucoside (caffeic acid cofactor) with their anthocyanin precursor to evaluate the role of the pyranoanthocyanin C10 substitution on stability. Pyranoanthocyanins exhibited absorbance half-lives ~2.1–8.6 times greater than cyanidin-3-glucoside, with ~15–52% of their original pigment remaining after 12 h of 90 °C heating at pH 3.0. 10-Methyl-pyranocyanidin-3-glucoside was the most stable (p < 0.01) based on UHPLC-PDA analysis, while 10-catechyl-pyranocyanidin-3-glucoside had the most stable color in part due to contribution from a colored degradation compound. Protocatechuic acid formed in all heated samples, which suggested a similar degradation mechanism among pigments. In conclusion, the C10 substitution impacted the extent of pyranoanthocyanin stability and the degradation compounds formed.