This study is significant for its applicability in screening tomato varieties under the protected cultures of the Jordan Valley with pest management practices. The experiment aimed to compare the performance of three tomato varieties (Dafnis, SV4129, and Newton) grown in the protected cultures of the Jordan Valley in terms of yield, and resistance to fungal diseases and viral infections. The varieties selected are among the most preferred varieties in the Jordanian market and are widely adopted by local growers. The research evaluated yield and key quality traits, including plant vigor, internode length, flowering, and fruit set, as well as important plant and fruit characteristics for each variety. The varieties were cultivated under greenhouse conditions in the Jordan Valley over one growing season, from 1 October 2023 to the end of March, with a growth period of approximately 150 days. The highest yield was obtained from the Newton cultivar. The results indicated that Dafnis and SV4129 exhibited strong resistance to Pythium, Fusarium, and the viral diseases Tomato Yellow Leaf Curl Virus (TYLCV) and Tobacco Mosaic Virus (TMV). Based on these findings, Newton is recommended for cultivation under protected conditions in the Jordan Valley, where effective virus management is in practice. However, in production systems with inadequate virus control, the adoption of the Newton cultivar is not advised due to its higher susceptibility to viral infections.