The paper is aimed at studying the methodological aspects of assessing the features and advantages of implementing climate-neutral investment projects in the context of environmental protection and energy security. For this purpose, investigation is focused on the performance of investment projects in nature resource sectors (agriculture, forestry, etc.) that provide renewable resources (biomass) for the generation of green energy. The paper identifies the peculiarities of the transition to low-carbon economy and creation of carbon markets as platforms for the development of a system for managing climate-neutral investment projects. The scientific novelty of this research lies in the improvement of approaches to substantiating the economic feasibility of investments in nature resource sectors in view of the climate change. Namely, a comprehensive approach to comparing alternative variants of investment project solutions in climate-neutral projects is suggested. Moreover, the developed methodological recommendations account for the variable meteorological factors in calculating economic indicators. The paper’s practical value can be seen in the determination of the benefits from the implementation of climate-neutral projects using the example of production and processing of the agro-biomass for the development of renewable energy based on the circular use of resources.