Background and Objectives: IBS is the most common functional disease of the low gastrointestinal tract. Recently, the interest towards a diet approach has increased, for example, a diet with low content of fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAPs). The aim of the present study is to evaluate the efficacy of a low FODMAP diet and a specific carbohydrate diet (SCD) conducted for 3 months on symptoms and to evaluate the deficiencies of vitamin D and folic acid in patients affected by IBS, matching the Rome IV criteria. Methods: We evaluated 73 patients divided into 2 groups: one submitted to low FODMAP diet and one to SCD, for 3 months. Patients were assigned to one of the 2 groups randomly and blinded. All the patients filled a visual analogue scale (VAS) to evaluate the severity of symptoms and a diary to evaluate the number of days with symptoms, and this was repeated after 3 months. Final evaluation was made by a blinded investigator. Results: In the end, the patients with low FODMAP diet had a significant improvement in bloating and distension (P = 0.000); the group with SCD instead had a low but not a significant improvement. One way ANOVA showed comparable severity of symptoms in the 2 groups pre-diet (P = 0.215), but a difference in the same symptoms after 12 days (P = 0.000). Tukey test showed a significant improvement in the low FODMAP diet group and only a trend of improvement in the second group of SCD. The vitamin D mean value in both groups at the time of enrollment was 38 ng/mL; in the end, the mean value in the low FODMAP diet group was 32 ng/mL and in the SCD group was 22 ng/mL, with a statistically significant difference. The folic acid mean value at the time of enrollment was 18 mg/dL; in the end, the mean value in the low FODMAP diet group was 15 mg/dL and in the SCD group was 8 mg/dL, with a statistically significant difference. Conclusion: Patients affected by IBS seem to have benefitted from a low FODMAP diet but not from an SCD, and a low FODMAP diet doesn't seem to cause vitamin D and folic acid deficiencies.