As “Curator of Experiments” for the early Royal Society, Robert Hooke (1635-1703), embodied the Baconian ideal of natural science. He tirelessly collected observations, devised and performed experiments, and invented or improved scientific instruments. Along with his practical engagements, Hooke also developed his own theories on phenomena ranging from the nature of light to the origin of fossils. Scattered throughout his writings, we also find methodological reflections. Though broadly Baconian, Hooke also added his own insights, leading to a specific take on the proper method for conducting science. In this essay, I discuss Hooke’s views on the brain in relation to his views on the proper method of observing nature, and his views on the organisation of matter as found in his landmark Micrographia. I will show how Hooke conceptualises the brain as a kind of mirror of nature. This will allow him to develop an optimistic empiricist view on the generation of ideas and our knowledge of nature.