The shedding of leaves, branches, flowers, and young fruit; scuffing of bark; and exposed roots that are caused by trunk or canopy shakers during harvest appears to be unavoidable, but generally does not reduce long-term yields. Nonetheless, such visible injuries have limited the widespread adoption of mechanical harvesting in Florida's citrus industry. We determined if such physical injuries caused by a properly operated trunk shaker resulted in any physiological injures or any consequent decline in vigor and productivity of well-managed, healthy citrus trees. We continuously monitored various physiological indexes in mature `Hamlin' and `Valencia' orange trees annually harvested by hand or by a linear-type trunk shaker with various shaking durations. Trunk shaking did not reduce return bloom, fruit set, young fruit growth, or canopy and root growth. There was a correlation between the seasonal timing of a simulated bark injury and recovery from the injury. Although some root exposure was frequently observed during trunk shaking, leaf water relations and fine root growth were unaffected. There was no difference in leaf dry weight per area and leaf nitrogen among treatments. Mechanical and hand harvesting in late season `Valencia' during full bloom removed similar amounts of flowers. However, immature fruit were removed by trunk shaking when `Valencia' were harvested after mid-May, and the number of young fruit removal increased with shaking duration and fruit size. The loss of young fruit for the next crop remains a major problem of mechanical harvesting in late harvest `Valencia'.