Given the importance of understanding health outcomes at fine spatial scales, iterative proportional fitting (IPF), a form of small area estimation, was applied to a fixed number of health-related variables (obesity, overweight, and diabetes) taken from regionalised 2019 survey responses (n = 5474) from the Idaho Behavioral Risk Factor Surveillance System (BRFSS). Using associated county-level American Community Survey (ACS) census data, a set of constraints, which included age categorisation, race, sex, and education level, were used to create county-level weighting matrices for each variable, for each of the seven (7) Idaho public health districts. Using an optimised modeling construction technique, we identified significant constraints and grouping splits for each variable/region, resulting in estimates that were internally and externally validated. Externally validated model results for the most populated counties showed correlations ranging from 0.79 to 0.85, with p-values all below 0.05. Estimates indicated higher levels of obesity and overweight individuals for midsouth and southwestern Idaho counties, with a cluster of higher diabetes estimates in the center of the state (Gooding, Lincoln, Minidoka, and Jerome counties). Alternative external sources for health outcomes aligned extremely well with our estimates, with wider confidence intervals in more rural counties with sparse populations.