Supplementation with iron and folic acid is widely recommended in women of childbearing age and during pregnancy; however, the effect of such supplementation on mineral status is not well-known. The aim of this study was to determine the effects of oral iron and folic acid, administered together and separately, on copper, zinc, calcium, and magnesium concentrations in the tissues of rats with a deficiency of both these micronutrients. The experiment was performed on 8-week-old female Wistar rats. In the first stage of the experiment, the animals were randomly assigned to a control group of rats fed the standard diet (AIN-93 M), and to a study group of rats fed a diet deficient in iron and folate. The study group was then randomly divided to four groups: group D was fed a deficit diet, group FE was fed a deficit diet with iron gluconate, the FOL group was fed a deficit diet with folate acid, and the FEFOL group was fed a deficit diet with iron gluconate and folate acid. After 2, 10, and 21 days of the intervention, ten animals from each group were killed. Mineral concentrations were assayed in the liver, spleen, pancreas, heart, and kidneys using atomic absorption spectrometry. Statistical analysis was performed using Statistica 12.0 with the ANOVA test (p < 0.05). It was found that separate supplementation with iron and folic acid significantly decreased copper concentrations in tissues. The deficit in iron and folic acid decreased, and their simultaneous supplementation increased calcium content in the organs. Separate and simultaneous supplementation decreased magnesium status in deficient rats. In conclusion, iron and folic acid, supplemented separately or simultaneously, affect the copper, calcium, and magnesium level in tissues.