Field evaluations are essential for determining the nutritional value of potatoes in their natural conditions, providing important information on nutrient levels shaped by diverse environmental and agricultural factors. This is particularly significant for rural communities that depend on this crop as their primary dietary staple and source of nutrients. This study assessed the concentrations of iron, zinc, and calcium in potatoes cultivated in Moquegua, an underexplored region in southern Peru, thus addressing a geographic gap in the nutritional profiling of potatoes across Peru’s diverse agricultural landscapes. To this end, popular potatoes from both native and modern varieties (n = 144) were harvested at elevations ranging from 58 to 3,934 m above sea level. The analysis was conducted using inductively coupled plasma mass spectrometry (ICP-MS). The soils associated with these varieties were also analyzed by inductively coupled plasma optical emission spectrometry (ICP-OES). The findings show that modern potatoes have a higher mean concentration of iron (7.858 mg/kg) and calcium (76.43 mg/kg), while native potatoes exhibit a higher concentration of zinc (3.389 mg/kg). Only moderate correlations were found among soil nutrients, as well as between iron and calcium contents in potatoes (p < 0.001). A principal component analysis (PCA) revealed that two principal components explain over 80% of the variance in both potato and soil samples across varieties. Iron is the main factor structuring micronutrient variability in potatoes, characterizing 85.4% of samples by relatively low Fe concentrations within the observed range. In soils, iron has the greatest influence on data variability for both modern and native potatoes, with zinc additionally affecting native potato soils. These findings enhance the understanding of the variability in micronutrient content and establish a baseline for future research aimed at improving the nutritional profiles of potatoes cultivated in this region, ultimately supporting local dietary needs and contributing to the assessment of the role that potatoes play in the daily diet of rural communities.
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