Pecan (Carya illinoinensis) is a tree nut native to North America. Although inhibited light exposure (most specifically as a result of overlapping tree canopies) has been shown to impair yield, the effect of this factor on nut antioxidant properties remains unknown. This study investigated effects of mechanical pruning and canopy height position of fruit on pecan kernel antioxidant contents and capacity. Beginning in 2006, trees in a ‘Western’ pecan orchard in New Mexico were subjected to three mechanical pruning frequency treatments (annual, biennial, and triennial) paralleling conventional practices, while other trees were maintained as unpruned controls. During the 2012 to 2014 seasons, pecans were sampled at fruit maturity from three canopy height zones (“low,” “middle,” and “high,” corresponding to 1.5 to 3.0 m, 3.0 to 4.5 m, and 4.5 to 6.0 m above the orchard floor). In vitro phenolics contents and antioxidant capacities of the nutmeats were evaluated by total phenolics content (TPC) and oxygen radical absorbance capacity (H-ORACFL), respectively. Soluble ester- and glycoside-bound phenolics were quantified by reversed-phase high-performance liquid chromatography (HPLC). For both TPC and H-ORACFL, results determined pruned samples had significantly higher values than unpruned samples (P < 0.001 for both comparisons), and that samples of “high” canopy height were significantly greater than those of “middle” height, which were in turn greater than those of “low” height (P < 0.001 for all comparisons). HPLC findings showed that in all three phenolic fractions (free, esterified, and glycoside-bound phenolics), nuts acquired from pruned trees had substantially greater concentrations of ellagic acid and its derivatives. Our findings indicate mechanical pruning of pecan trees and higher tree canopy position of fruit increase nut antioxidant properties.