The crucial step-wise changes in the geochemical evolution of Earth’s crust, ocean, and atmosphere can be explained assuming low-energy nuclear reactions (LENR) triggered by the tectonic and seismic activities. The phono-fission reactions are related to Fe and Ni as starting elements, to medium-weight elements (Mg, Al, Si) as intermediate resultants, and to C, N, O as final resultants. Geochemical data and experimental evidence support the phono-fission conjecture. A spectral analysis over the time interval 1955–2013 shows common cycles (same periods) between atmospheric CO2 growth rate and worldwide global seismic-energy release rate, whereas the trending increasing behavior of the atmospheric CO2 is in response to the anthropogenic activities. Investigating on the correlation between such seismic and atmospheric time-fluctuations, the latter can be explained by cyclic worldwide seismicity triggering phono-fission reactions massively in the Earth’s crust. In this framework, LENR from active faults and volcanoes can be considered as a consistent cause for carbon dioxide time-oscillations. Such a partial and natural carbon production is to be taken into a serious account when discussing about climate change.