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What agronomy has to say about fertilizers is far from straightforward, from praising the virtue of chemical fertilizers and criticizing peasant routine, to rejecting all chemicals and promoting organic fertilization, with more moderate positions in-between, calling for a close association between both chemical and organic fertilizers. Agronomists devote a very large share of their works to this issue of fertilization, dealing with soil amendments as well as chemical fertilizers. The present paper aims at exploring how agronomists rationalized the techniques of soil fertilization while adapting to the rise of agrochemistry over the 19th century, using three significant examples, the analysis of which will combine rural history, the history of science and technology, and environmental history. As our first example, we chose saltpeter production, analyzed by Boussingault at the beginning of the 1860s; second, we turn to sewage waters coming from urban draining pits, used as agricultural fertilizers, and studied by Dehérain; and lastly we focus on the rise of chemical fertilizers and of the fight against fraud, using texts by Grandeau.