Background: Decreased bone mineral density (BMD) is a common problem among patients with inflammatory bowel disease (IBD). We hypothesised that an insufficient intake of folate might affect BMD. Methods: The study subjects included 26 with Crohn’s disease—CD, 30 with ulcerative colitis—UC, and 31 healthy adults (control group—CG) aged 18–50 years. Participants were asked to follow their usual diet, and dietary intake was assessed by a 4-day, 24 h dietary recall. All the participants filled in a questionnaire referring to folic acid supplementation. The BMD, T-score, and Z-score of the lumbar spine (L1–L4) and femoral neck (FN) were assessed. Results: We found significant differences in the body mass, BMI (body mass index), CRP (C-reactive protein), BMD, Z-score, and T-score of the L1–L4 and FN between groups. There were no differences in energy and folate intake or the percentage coverage of recommended dietary allowances (RDA) of folate in all groups. Moreover, 70% of patients with UC, 92% of patients with CD, and 77% of CG patients showed insufficient folate intake. Folic acid was supplemented with a similar frequency in patients covering and not covering the RDA of folate. The intake of folate per 1000 kcal correlated positively with the CD group’s BMD and T-score of L1–L4. Conclusions: Insufficient folate intake is common in patients with IBD and healthy individuals. The impact of folate on BMD in IBD is not clear. We need more studies on the association between folate intake, folic acid concentration, and BMD in IBD.