Isaac Newton condemned the use of hypotheses with his (in)famous methodological statement, Hypotheses non fingo, and yet employed hypotheses explicitly in every edition of the Principia. Some commentators have argued that Newton was working with several inconsistent notions of ‘hypothesis’: specifically, the hypotheses he used in the Principia are not the sort that he railed against in the General Scholium at the end of that book. Other commentators argue that Newton’s methodological statements are simply inconsistent with how he actually proceeded: for example, they argue that the queries introduced by Newton at the end of his Opticks are hypotheses-in-disguise. I argue that Newton’s methodological pronouncements and his use of hypotheses are far more consistent than previously thought. I consider Newton’s methodology within the framework of his three-way epistemic distinction between theories, which are certain and experimentally confirmed, hypotheses, which are uncertain and speculative, and queries, which are not certain, but provide the proper means to establish the certainty of theories. I call this division Newton’s ‘epistemic triad’. I argue that Newton’s hypotheses and queries have distinctive and vital supporting roles within this epistemic triad. This provides us with a much more consistent picture of Newton’s methodology. Drawing together the strands of Newton’s methodology over the forty-odd years of his active scientific life, I defend three theses in relation to Newton’s epistemic triad: Endurance thesis. There are some general features of Newton’s methodology that do not change. These are characterised by the framework of the epistemic triad. Developmental thesis. There are some particular features of Newton’s methodology that change over time. These can be characterised as a development (and/or fine-tuning) of the epistemic triad. Contextual thesis. There are some particular features of Newton’s methodology that vary with respect to context (i.e. the topic of inquiry). These can be characterised as an adaptation of the epistemic triad to particular contexts.