This study evaluated the effect of pearl millet subjected to different processing on the intestinal health of rats. The animals were fed a standard iron-free diet (28 days) (hemoglobin depletion: 8.65 + 1.40 g/dL of hemoglobin). Subsequently, they were divided into four groups for hemoglobin repletion (21 days): standard diet + ferrous sulfate (SD + FS); standard diet + non-germinated open-pan cooked millet flour (SD + NGOPCMF); standard diet + germinated open-pan cooked millet flour (SD + GOPCMF); and standard diet + extrusion-cooked millet flour (SD + ECMF). Hemoglobin level did not differ among groups. The SD + NGOPCMF, SD + GOPCMF and SD + ECMF groups demonstrated a higher Chao index in the microbiome and a higher number and area of goblet cells and longitudinal muscle layer width. The SD + NGOPCMF and SD + GOPCMF groups demonstrated increased cecum weight, crypt depth, crypt thickness, and circular muscle layer width; lower fecal pH; and a higher relative abundance of Bacteroidota, while the SD + FS group showed the highest abundance of Actinobacteriota. The SD + GOPCMF group stood out for showing the lowest fecal pH, better α-diversity (Chao and Shannon index), and the highest width of the longitudinal muscle layer. In conclusion, pearl millet subjected to different processing, mainly germination, has the potential to improve the composition of the intestinal microbiota and the intestinal morphology in rats induced to iron deficiency.