Peaches and apricots contain significant quantities of phenolics and carotenoids, components with various health benefits. Fruit peel has been found to possess high concentrations of these compounds yet is often removed prior to canning. We studied how phytochemical content and composition were affected by peeling in three peach and three apricot varieties. Peeling decreased carotenoid content while its effect on phenolic content and antioxidant capacity in both fruits was variety dependent. Significant diffusion of phenolics into syrup was found (> 30%) while leaching of carotenoids was minimal (< 1%). Unpeeled canned fruit and its syrup, compared to peeled samples, had greater phenolic and carotenoid content post-processing and after 6 months storage at 20 °C. HPLC analysis showed that flavonol glycosides and β-carotene decreased most with peeling; zeaxanthin completely degraded in storage. Fruit and syrup phenolic content equilibrated over time, showing > 20% losses after 6 months. Losses of carotenoids were > 38%, being more severe in peeled fruit. Our results indicate that peeling decreased the phytochemical, particularly carotenoid, content of canned peaches and apricots but canned apricots were still excellent sources of vitamin A after 6 months of storage. Consumption or secondary use of syrup would be important to increase total phenolic intake from canned fruit.