The study of the physical processes that drive the variability of the Earth's climate system is one of the most fascinating and challenging topics of research today. Perhaps the largest uncertainties in our ability to predict climate change are the cloud formation process and the interaction of clouds with radiation. Here we show that in the southern Pacific Ocean cloud effects on the net radiative flux in the atmosphere are related to the intensity of the Earth's magnetic field through lower atmosphere cosmic ray effects. In the inner region of the Southern Hemisphere Magnetic Anomaly (SHMA) it is observed a cooling effect of approximately 18 W/m2 while in the outer region it is observed a heating effect of approximately 20 W/m2. The variability in the inner region of the SHMA of the net radiative flux is correlated to galactic cosmic rays (GCRs) flux observed in Huancayo, Peru (r = 0.73). It is also observed in the correlation map that the correlation increases in the inner region of the SHMA. The geomagnetic modulation of cloud effects in the net radiative flux in the atmosphere in the SHMA is, therefore, unambiguously due to GCRs and/or highly energetic solar proton particles effects.