Anaemia and bone metabolism alterations are common in inflammatory bowel disease (IBD), which is a heterogeneous group of diseases that include Crohn's disease (CD) and ulcerative colitis (UC) with a rich intestinal and extraintestinal symptomatology. All these make the diagnostic procedures complicated and difficult. The aim of this study was to assess the effect of parenteral iron administration on biomarkers of mineral and bone homeostasis over time. The study was a single-centre non-randomised prospective study. It was carried out between 2016 and 2020 in a group of patients in the Department of Internal Medicine and Gastroenterology Subunit of Inflammatory Bowel Diseases at the National Institute of Medicine of the Ministry of the Interior and Administration in Warsaw. At the first examination, the baseline disease severity, initial evaluation of anaemia (morphology, iron (Fe), total iron binding capacity (TIBC), ferritin, vitamin B12, folic acid) and bone mineral metabolism including C-reactive protein (CRP), albumins, alkaline phosphatase (ALP), Calcium, osteocalcin, phosphate in serum and in urine, parathyroid hormone (PTH), vitamin D3, fibroblast growth factor (iFGF23) and procollagen type 1N propeptide (P1NP) C-terminal telopeptide (CTX), was initially assessed. On the basis of peripheral blood counts, an appropriate dose of iron (iron derisomaltose or caboxymaltose) was administered. During the subsequent appointments on week 1, 4, and 12 morphology, iron (Fe), total iron binding capacity (TIBC), ferritin, vitamin B12, folic acid, C-reactive protein (CRP), albumins, alkaline phosphatase (ALP), Calcium, osteocalcin, phosphate in serum and in urine, parathyroid hormone (PTH), vitamin D3, fibroblast growth factor (iFGF23) and procollagen type 1N propeptide (P1NP) C-terminal telopeptide (CTX), were evaluated. A total of 56 patients were enrolled into the study: 24 women and 32 men. In the group, 32 patients had Crohn's disease (CD) and 24 had ulcerative colitis (UC). We found a statistically significant increase in the concentration of albumin (p = 0.031), haemoglobin (p < 0.001), haematocrit (p < 0.001), MCV (p < 0.001), MCHC (p = 0.001), iron (p < 0.001) and ferritin (p < 0.001) after the administration of parenteral iron. The influence of individual iron formulations on the analysed parameters (phosphate concentration in serum and in the urine, iFGF23, P1NP, PTH, vitamin D, haemoglobin and ferritin) was similar. Interestingly, an inverse correlation was found between the concentration of phosphorus in the blood and iFGF23 at certain time-points; however, in the study group they did not significantly affect the disturbances of calcium and phosphate metabolism. In the study group, transient and non-significant disorders of phosphate metabolism were found, which does not constitute a contraindication to treatment with parenteral iron in inflammatory bowel disease patients, which was safe and efficient.