Organic tomato cultivation is growing all over the world due to its healthy functional properties and environmental concerns. Recently, some new varieties with increased functional properties, particularly high lycopene, have been developed. However, few were assessed under organic farming systems. The objective of this study was to evaluate physico-chemical properties and the main bioactive compound contents, as well as lipophilic, hydrophilic and total radical scavenging activities of a recently developed high lycopene tomato variety homozygous for hp-2dg genes (HLT-F71) grown under organic conditions for two non-consecutive years (2019 and 2021) compared to the ordinary control ‘Nemador’ variety. The lycopene, β-carotene, total phenol, flavonoid, vitamin C, radical scavenging activity and tocopherols were analyzed by using spectrophotometric and HPLC methods, respectively. The high lycopene content variety presented suitable marketable yield, average fruit weight, pH, titratable acidity, firmness and higher °Brix, pulp color than the control. Additionally, it has significantly higher lycopene, β-carotene, total phenol, flavonoid, vitamin C and particularly considerable α-tocopherol contents, as well as radical scavenging activity. The high lycopene tomato variety with hp genes proved to be an effective sustainable variety for enhancing tomato fruit yield and functional properties even under organic grown conditions.