Reducing emissions from power systems requires enhancing the penetration of non-conventional renewable energy sources (NCRE) in the generation mix. However, such penetration requires high levels of operational flexibility in order to ensure an adequate balance between generation and demand. Concentrating solar power plants with thermal storage (CSP-TES) and battery energy storage systems (BESS) have shown to possess technical characteristics compatible with such high flexibility requirements. However, due to the high capital costs of these technologies, decision-makers must seek for cost-effective configurations and operation modes. This study presents the development of a methodological framework for designing the long-term transition of a multi-regional energy system towards a low carbon emission system. The sought system is characterized by a high penetration of NCRE, and the use of CSP-TES, BESS and electricity transmission settings for providing effective levels of operational flexibility. For this, the transformation of the Chilean electricity system between the years 2018–2050 is studied, using a tailored modification of the well-known OSeMOSYS optimization tool for energy systems planning. The main results indicate that by 2050, and considering a baseline scenario defined for 2016, for most of the scenarios studied the renewable electricity generation would be at least a 90 % and CO2 emissions would be 75 % lower. Furthermore, it is shown that providing operational flexibility to the system requires a mixed generation from hydroelectric reservoirs, CSP-TES plants, BESS, pumped-storage hydropower and natural gas generators. The obtained results allow planning the capacity and operation of CSP and BESS plants, which are adapted to the future flexibility requirements of the Chilean electric power system. Incentive policies like stimuli to growth BESS, would favor primarily the photovoltaic growth of the system at the expense of CSP-TES capacity, while CSP-TES growth incentives would maintain photovoltaic generation levels, but would decrease Wind and natural gas generation.