This research assessed fruit load management and production techniques for cultivating indeterminate tomatoes in a high tunnel under intensive organic management. The successful production of high-quality, high-yielding crops is important for fruit and vegetable producers, especially growers using high tunnels. High tunnels are well-suited to organic farming and can be used to grow many valuable specialty crops. Fruit load management is practiced in fruit production (e.g., apples, peaches, and grapes), but there is lack of consensus concerning the effectiveness of fruit cluster pruning on tomato (Solanum lycopersicum) and its impact on fruit yield, quality, and marketability. In addition, there is no published research on tomato cluster pruning in certified organic systems or intensively managed high tunnels (e.g., densely planted, trellised, vegetatively pruned plants) for the Front Range of Colorado. In 2016 and 2017, a randomized complete block design was used to test the effects of cluster pruning within a high tunnel on certified organic land at Colorado State University’s (CSU’s) Agricultural Research, Development, and Education Center, South. Two treatments and three tomato cultivars were selected for the study; the treatment–cultivar combinations were replicated six times within a high tunnel. The treatments involved reducing fruit loads to three fruit and six fruit per cluster, whereas plants with unpruned clusters, which naturally developed as many as 10 fruit, served as the control. Tomato cultivars evaluated were ‘Cherokee Purple’, a widely studied heirloom, and two hybrids: ‘Jet Star’ and ‘Lola’. Parameters measured included total yield, individual fresh fruit weight, soluble solids content (SSC), marketable yield, and nonmarketable yield. Individual fresh fruit weight increased for both hybrids in the three-fruit treatment, averaged over two growing seasons. ‘Cherokee Purple’ did not respond to the cluster pruning treatments. There was no decrease in total yield, across all cultivars, between treatments and the unpruned control. However, ‘Jet Star’ yielded more than the other two cultivars. In addition, SSC and marketability measurements were more influenced by cultivar than cluster pruning treatments. ‘Lola’ had a significantly greater SSC than the other two cultivars. ‘Jet Star’ had the greatest marketable yields of all cultivars tested whereas ‘Cherokee Purple’ produced greater nonmarketable (cull) yields. Cluster pruning produced larger organic tomatoes without reducing yield or quality for two of the three cultivars used in the study. Cultivar selection remains one of the greatest factors in determining yield, quality, and marketability of a crop.