Long after its alleged demise, phlogiston was still presented, discussed and defended by leading chemists. Even some of the leading proponents of the new chemistry admitted its ‘absolute existence’. We demonstrate that what was defended under the title ‘phlogiston’ was no longer a particular hypothesis about combustion and respiration. Rather, it was a set of ontological and epistemological assumptions and the empirical practices associated with them. Lavoisier's gravimetric reduction, in the eyes of the phlogistians, annihilated the autonomy of chemistry together with its peculiar concepts of chemical substance and quality, chemical process and chemical affinity. The defence of phlogiston was the defence of a distinctly chemical conception of matter and its appearances, a conception which reflected the chemist's acquaintance with details and particularities of substances, properties and processes and his skills of adducing causal relations from the interplay between their complexity and uniformity.