In this 2-year study, ‘Brown Snout’ specialty cider apples (Malus ×domestica) that had been hand harvested or machine harvested with an over-the-row shake-and-catch small fruit harvester were ambient stored (56 °F mean temperature) for 0, 2, and 4 weeks to evaluate yield, fruit damage, yield loss, and juice quality characteristics. The average yield (pounds per acre) of fruit picked and retained by the mechanical harvester was 74% that of the hand-harvest yield and 81% that of the hand-harvest yield when fruit that fell out of the harvester was included in the machine-harvest yield. Percent fruit bruised and cut were greater for machine harvest (97.5% and 25.5%, respectively) than for hand harvest (47% and 0.5%, respectively), on average for 2014 and 2015. Yield loss to rot was greater for machine harvest than for hand harvest, and increased for both methods over time; percent rot doubled from 2 to 4 weeks storage for machine harvest (22% to 41%), and while negligible, tripled from 2 to 4 weeks storage for hand harvest (0.7% to 2.1%). Juice quality characteristics did not differ due to harvest method, but did differ due to year and storage time. Soluble solids concentration [SSC (%)] and specific gravity (SG) did not change due to storage in 2014, but in 2015, SSC and SG were greater on average for 2 and 4 weeks storage duration (15% and 1.062, respectively) than at harvest (13.31% and 1.056, respectively). Titratable acidity (grams per liter malic acid) decreased in 2014 from 2.98 g·L−1 at harvest to 2.70 g·L−1 on average for 2 and 4 weeks storage duration, but did not differ due to storage in 2015. Tannin [tannic acid equivalent (%)] was unchanged in 2014 from harvest to 4 weeks storage, but increased in 2015 from 0.16% at harvest to 0.19% by 4 weeks storage. These results indicate that harvest efficiency could be improved with some engineering modifications of the over-the-row mechanical harvester and training modifications for the trees. A comparison of the aromatic and phenolic contents of mechanically harvested and hand-harvested ‘Brown Snout’ would be a valuable next step in evaluating shake-and-catch mechanical harvest technology for cider apple production.