Global climate change is the uppermost challenge for agriculture nowadays. The increase of temperatures, most of the time accompanied by a reduction of water availability, has a negative impact in plant growth and ultimately in crop production. Moreover, the growing population rate poses a huge concern on food availability and safety in this context of climate change. Tomato (Solanum lycopersicum L.) is a major vegetable crop highly appreciated by its nutritional qualities. Over the past decades, huge efforts have been made to genetically improve this species through breeding activities mainly directed to the development of varieties adapted to high input traditional systems instead of organic low input farming. Thus, the combined action of climate change and the consumers demand on greener and safer agricultural practices, makes necessary the development of varieties suitable for organic production under the climate change scenario. Funded by the European Union´s Horizon 2020, the BRESOV project aims to the development of new tomato varieties better adapted to climatic adverse conditions and to organic agriculture. The present work includes the implementation of a successful breeding programme which has allowed to obtain new inter- and intra-specific tomato hybrids. Their agronomic potential as rootstocks was tested under organic conditions, and BT02530 x BT00120, BT08300 x BT00250 and BT02220 x BT00230 hybrids were found to show higher fruit yield when compared to commercial rootstock hybrids. These hybrids also showed better agronomic performance under stress conditions, providing a suitable material for increasing resilience of organic tomato farming to climate adverse conditions.