Designing a cost-effective portfolio of micronutrient intervention programs is complex and generally undertaken with limited data. We developed the MINIMOD-Secondary Data (MINIMOD-SD) tool, which uses household consumption and expenditure survey data and other secondary data to estimate apparent nutrient intakes and model the effectiveness and cost-effectiveness of micronutrient intervention programs. We present the SD tool methodology and results in the context of Cameroon, with a particular focus on vitamin A (VA) for children and folate for women of reproductive age (WRA). We compared the MINIMOD-SD tool estimates with those of the full MINIMOD tool, which uses 24-h dietary recall data. Qualitatively, however, the two tools were generally consistent in predicted subnational patterns of micronutrient adequacy and identification of effective and cost-effective (cost per child/WRA moving from inadequate to adequate intake) interventions. Secondary data and the MINIMOD-SD tool can provide policymakers with information to qualitatively assess deficiency risks and identify cost-effective interventions. However, accurately quantifying individual-level deficiency or dietary inadequacy and intervention effectiveness and cost-effectiveness will likely require individual-level dietary data and biomarker measurements.