Iron is deficient in the milk of most dairy species including cows and goats; therefore, iron fortification is desirable in milk and dairy products to increase dietary iron levels. Ferrous sulfate (FeSO₄) is reportedly the most preferable form of iron salts for iron fortification as it provides high bioavailability. No report has been available for iron recovery and microstructural distribution of iron in FeSO₄ fortified cheeses, especially in caprine cheeses. The purposes of this study were to determine the recovery of iron, and locate microstructural loci of iron in iron-fortified caprine milk cheeses. Three batches of 3 types of goat Cheddar cheeses were manufactured, and stored at 2 temperatures (4°C and −18°C) for 0, 2 and 4 mo. Three cheese types were control cheese (CC) without Fe addition, and 2 types of iron fortified cheeses with regular ferrous sulfate (RFS) and large microencapsulated ferrous sulfate (LMFS) by 8.23g and 9.03g per 9 kg cheese, respectively, considering 16% Fe in FeSO₄ for both types of fortifications. All cheese samples were analyzed for microstructure and Fe loci of samples by scanning electron microscopy (SEM, S-3400N II, Hitachi, Japan). SEM samples were initially fixed with 2% glutaraldehyde and 1% of osmium tetraoxide (OsO₄) in 0.05 M phosphate buffer for 10 min, followed by a series of acetone dehydrations with increased concentrations and times, placed in liquid CO₂ for critical point drying, and then were gold coated by sputter coating. Results showed that iron contents of CC, RFS and LMFS cheeses were 0.0162, 0.822, 0.932 mg Fe/g cheese, respectively, indicating that Fe levels substantially increased iron in both fortified cheeses. Respective Fe recovery rates for LMFS and RFS cheeses were 73.5 and 71.9%. Cheese microstructures revealed that LMFS contained smaller, elongated and sharp-edged Fe particles, while RFS showed bigger, wider and rectangular Fe particles. The aggregated iron particles became clearly visible from proteolyzed casein networks as storage time advanced. It was concluded that SEM analysis was able to identify iron loci and its concentration in the Fe fortified caprine cheeses.