Iron fortification compounds are of special interest to treat iron deficiency anemia, however, the dose-response effects of these fortificants on liver and renal functions have not been extensively reported in human subjects. The present study determines the effects of prebiotics and iron fortificants on liver function tests (LFTs) and renal function tests (RFTs) among women of reproductive age (WRA). A double-blind randomized controlled trial was performed for the duration of 90 days. A total of 75 iron-deficient women were selected and randomly divided into 5 groups (4 treatment groups and 1 control group). For this purpose, four different types of fortified wheat flour were prepared using two iron fortificants (NaFeEDTA and FeSO4) and two prebiotics (Inulin and Galacto oligosaccharides) were given to four treatment groups, while control groups were only given iron-fortified flour without the addition of prebiotics. Blood samples were collected every month to evaluate Liver Function Tests, including Alanine Transaminase (ALT), Aspartate Transaminase (AST), Alkaline Phosphatase (ALP), total bilirubin and Renal Function Tests, including serum urea and creatinine. Our results found that prebiotic and iron-fortified diets increased ALT, AST and total bilirubin levels among WRA. For AST, ALP and total bilirubin, our results found the highest increase in the treatment groups treated with prebiotics and iron fortificants at 963 mg/kg GOS + 15 ppm FeSO4. Moreover, the highest values of ALT and serum creatine were seen in groups treated with 963 mg/kg Inulin + 20 ppm NaFeEDTA, while maximum value for serum urea could be seen in the group given 963 mg/kg GOS + 30 ppm FeSO4. The study concluded that prebiotic and iron-fortified diets increased ALT, AST and total bilirubin levels among WRA.