A systems-based approach was used to evaluate integrated (IFP) and organic fruit production (OFP) (during and after the transition period) in an established high-density commercial orchard of disease-resistant ‘Liberty’ apples (Malus ×domestica Borkh.). Agroecological and economic evaluations included: yields, tree growth, leaf nutrient levels, arthropod and cosmetic fruit damage, environmental impacts, variable costs of production, and potential crop value using both direct market and wholesale market prices. Cumulative yields (2004–2007) of both harvested and total (harvested + dropped) fruit were not different between the two systems. Tree size (trunk cross-sectional area) was not consistently different between the production systems. The IFP-grown apples had between 3% and 6% insect damage (within normal percentages for this region) and between 3% and 17% total damage (either internal or cosmetic). The OFP-grown apples had between 3% and 25% insect damage and 3% to 75% total damage, varying greatly from year to year. In 2006, superficial blemishes, caused by diseases and scarfskin, were extensive on OFP-grown fruit. Using the Environmental Impact Quotient, the potential negative environmental impacts were estimated to be six times greater in the OFP system, largely as a result of the use of lime sulfur and fish oil for thinning and the large quantity of kaolin clay used for pest control. Partial budgets of both systems estimated variable production expenses to be 9% greater for OFP. Sales value was estimated to be 6% greater for OFP than IFP using direct market prices (e.g., farm stand or farmers' market) and 11% greater for IFP than OFP using wholesale market prices. A 56% premium was used to calculate the OFP crop value in the third and fourth years (fruit could have been sold with an organic label after 36 months from the last organically prohibited material). Four years of evaluation suggested that IFP could be widely implemented in the northeastern United States, but the lack of market incentives might impede its adoption. Producing disease-resistant apples under an OFP system also showed potential for success, but a price premium would be needed to offset the reduced profitability incurred from arthropod pests, poor fruit finish, and small fruit size.