Interest in unheated plastic film-covered high tunnels to extend the growing season of high-value fruits and vegetables is growing rapidly, but sustainable soil management in intensively managed high tunnels is challenging. Yields, fruit quality, and soil quality in transition organic and conventional tomato were measured over the course of three growing seasons. Nitrogen (N) was applied at the rate of 112, 168, and 224 kg total N/ha in the form of chicken manure compost to the organic treatments and a polymer-coated slow-release urea fertilizer in the conventional treatments. Marketable yield of organically grown tomatoes was lower in Year 1 but equaled conventional tomatoes in Years 2 and 3. Soil quality as measured by total carbon (C) and N and microbial activity was significantly greater in organic tomato production at the end of the study. Significant phosphorus (P) and potassium (K) applied with the composted manure resulted in high soil P and K levels in organically managed high tunnels after just 3 years of application. Although compost is the most economical organic fertilizer and results in significant benefits in soil quality during the transition phase to organic production, a maintenance fertility plan is needed once available soil P reaches adequate to high levels. Combinations of compost and high N, low P organic fertilizers are needed for optimum maintenance fertility strategy for organic tunnel house production.