Iron is one of three major minerals in human body. However, the iron deficiency is a medical problem in developed and underdeveloped countries due to its poor oral absorption or insufficient iron intake. Encapsulation could solve problems associated with oral iron consumption. Various advantages including low cost, biodegradability, biocompatibility and large-scale production have been included in the current study. In a modified encapsulation method, iron microparticles were prepared using low methoxy pectin and resistant starch during spray drying. Covalent and hydrogen bonds were formed between iron and pectin and between polymers, respectively. Particles sized 3.5 ± 1.14 μm and showed spherical shapes. The yield of particles was 72.07%, and solubility and loading efficiency were 33.64% ± 0.88 and 34.79%, respectively. In conclusion, using iron as a cross-linker of pectin molecules resulted in microparticles with appropriate properties of lowering organoleptic changes and a better bioavailability especially in dairy-based products for food fortification.