Between the mid-19th century and the mid-20th century, French biology, despite a handful of remarkable breakthroughs (e.g. Claude Bernard, Louis Pasteur), contributed only very marginally to the growth of biological thought. This has puzzled historians for decades, especially given the unbelievably strong opposition met by cell theory, evolutionary theory and genetics during that time in France. The aim of this paper is to show how a specific form of positivism was instrumental in shaping an epistemological attitude, shared by most scientists, that opposed any form of speculative theorization within biology. I show first that the French Society of Biology, which quickly became a highly influent institution, promoted exactly this kind of positivism, already epitomizing this position in its founding manifesto of 1849. Second, partly on the basis of secondary sources (Gley 1899, Schnitter 1992, Bange 2009), I document the kind of research that was promoted within that Society during the second half of the 19th century and especially from 1865 onwards, when Claude Bernard published his Introduction to the Study of the Experimental Medicine. An experimental-physiological approach to biology was particularly valued then, reducing theoretical explanation to only the identification of external causal parameters. In the final section, I argue that it was this dual and complex Comtian-Bernardian legacy that was captured by the term “positivism” within French biology. I especially focus on the fact that this positivism was a crude simplification compared to Comte’s and Bernard’s own subtle ideas. Unlike Comte, it made almost no room for the agency of organisms. Unlike Bernard, it minimized the significance of a third entity between an organism’s living parts and the environment, namely the “internal milieu".