Overcoming the long-standing distrust of ‘research’ is especially challenging within the colonial structures of Western science. This article aspires to rise to this challenge by conceptualising Pūtaiao as a form of Indigenous research sovereignty. Grounded in Kaupapa Māori Theory, Pūtaiao is envisioned as a Kaupapa Māori way of doing science in which Indigenous leadership is imperative. It incorporates Māori ways of knowing, being, and doing when undertaking scientific research. An essential element of Pūtaiao is setting a decolonising agenda, drawing from both Kaupapa Māori Theory and Indigenous methodologies. Accordingly, this centres the epistemology, ontology, axiology and positionality of researchers in all research, which informs their research standpoint. This approach speaks back to ontological framings of Western scientific research that restrict Indigenous ways of researching in the scientific academy. Furthermore, Pūtaiao offers tools and language to critique the academic disciplines of Western science which are a colonial construct within the global colonising agenda. As such, the theoretical search for Indigenous science(s) and Indigenising agendas explore the dialogical relationship between both knowledge systems – Kaupapa Māori science and Western science. This relationship necessitates setting a decolonising agenda before an Indigenising agenda can be realised, whereby they are mutually beneficial rather than mutually exclusive. This article is an affirmation of the work and discourse of Indigenous scientists. In this way, Pūtaiao becomes a pathway for asserting Indigenous sovereignty over and redefining scientific research for future generations of Māori and Indigenous researchers.