Local‐level data on the population's nutritional status are rarely available. For targeting, methods are needed to identify localities with populations at risk for nutritional deficiency. A method was developed that used biochemical (BIO), anthropometric (ANTHRO), intake, or socioeconomic (SES) data (with internationally recommended indicators & cutoffs) to identify localities at risk for iron, zinc, vitamin A or protein deficiencies in 11 Latin American countries. This method had several flaws: contradictory results when 2 ANTHRO indicators were used concurrently as recommended; difficulty in harmonizing BIO, ANTHRO & intake data (mostly at departmental level) with SES data (always at local level); & lack of data on recommended SES indicators. An improved method was developed: only BIO data are used to identify departments at risk for a specific nutrient deficiency; lacking BIO data, height‐for‐age Z score <‐2 is used to identify departments where populations are at risk for a nutritional deficiency (not nutrient‐specific); & SES data (poverty‐intensity index or proportion living in extreme poverty) are used in tandem with BIO or ANTHRO data to identify at‐risk localities within at‐risk departments. This method coupled with mapping software facilitates the identification of localities with nutritionally at‐risk populations. Funding: AgroSalud Project (CIDA), CIAT.