Methods for enumeration and population-based health assessment for First Nations, Inuit, and Metis (FNIM) living in Canadian cities are underdeveloped, with resultant gaps in essential demographic, health, and health service access information. Our Health Counts (OHC) was designed to engage FNIM peoples in urban centres in "by community, for community" population health assessment and response. The OHC methodology was designed to advance Indigenous self-determination and FNIM data sovereignty in urban contexts through deliberate application of Indigenous principles and linked implementation strategies. Three interwoven principles (good relationships are foundational; research as gift exchange; and research as a vehicle for Indigenous community resurgence) provide the framework for linked implementation strategies which include actively building and maintaining relationships; meaningful Indigenous community guidance, leadership, and participation in all aspects of the project; transparent and equitable sharing of project resources and benefits; and technical innovations, including respondent-driven sampling, customized comprehensive health assessment surveys, and linkage to ICES data holdings to generate measures of health service use. OHC has succeeded across six urban areas in Ontario to advance Indigenous data sovereignty and health assessment capacity; recruit and engage large population-representative cohorts of FNIM living in urban and related homelands; customize comprehensive health surveys and data linkages; generate previously unavailable population-based FNIM demographic, health, and social information; and translate results into enhanced policy, programming, and practice. The OHC methodology has been demonstrated as effective, culturally relevant, and scalable across diverse Ontario cities.