Facing global changes and the challenge of food security, scientists are being questioned by decision-makers and stakeholders on the sustainability of agro-systems. The main difficulty in dealing with this question is to obtain enough data over long periods of time. Monitoring slow drifts and weak noises is needed to forecast tipping points that can jeopardize the present steady state. High-resolution datations by radiocarbon coupled with detailed palynological determinations in sediments, historical archives on yields and crop quality, and high-frequency field in situ measurements give information on climatic changes from multi-secular to seasonal and hourly time scales. In the long term, climatic forcing dominates agriculture performance, at that time only organic agriculture, with oscillations between prosperity and misery driven by climate and intermediated by civilization flourishing and collapsing; in the medium term, in modern agriculture, irrigation provides a provisional buffering effect on yield and crop quality despite present warming; in the short term, either under non-fertilized forested ecosystem or intensive rice cropping, the same patterns are evidenced and point to the importance of soil microflora shifting from aerobiosis to anaerobiosis. In all cases, geochemistry offers appropriate tools to decipher the climate-soil-agriculture complex interplay.