Abstract Background Iron deficiency is common in patients with inflammatory bowel disease (IBD), where poor absorption or prior surgery often renders oral iron supplementation ineffective, necessitating intravenous (IV) iron therapy. Hypophosphataemia, particularly associated with ferric carboxymaltose via fibroblast growth factor 23 dysregulation, is a recognized complication of IV iron therapy. It can result in severe outcomes such as rhabdomyolysis, osteomalacia, fractures, and convulsions. This study evaluates the risk of hypophosphataemia between ferric carboxymaltose and other IV iron formulations and its association with complications. Methods This retrospective propensity-matched study utilised the TriNetX database, a global repository of de-identified electronic health records. The first analysis compared ferric carboxymaltose to other IV iron formulations (iron sucrose, sodium ferric gluconate, ferumoxytol, ferric derisomaltose), matched on demographics (age, gender, ethnicity) and comorbidities (vitamin D deficiency, malnutrition, malabsorption, diabetes, CKD by stage, alcohol abuse, hyperparathyroidism, corticosteroid, diuretic, antacid, and bisphosphonate use) to assess hypophosphataemia risk. The second and third analyses evaluated hypophosphataemia-related complications in ferric carboxymaltose versus other formulations, both in the general population and in patients with IBD. Results We compared 115,242 ferric carboxymaltose patients to those on other IV iron formulations. Ferric carboxymaltose was associated with higher odds of severe (OR: 2.84, 2.22–3.64, p<0.0001) and moderate (OR: 1.37, 1.29–1.46, p<0.0001) hypophosphataemia but lower odds of mild hypophosphataemia (OR: 0.84, 0.79–0.88, p<0.0001). Among 25,586 hypophosphataemic patients, those on ferric carboxymaltose had lower odds of acute complications within 3 months, including muscle weakness (OR: 0.57, 0.47–0.70, p<0.0001), rhabdomyolysis (OR: 0.38, 0.20–0.75, p=0.003), disorientation (OR: 0.53, 0.46–0.61, p<0.0001), convulsions (OR: 0.59, 0.48–0.73, p<0.0001), cardiac arrhythmias (OR: 0.61, 0.54–0.69, p<0.0001), and respiratory failure (OR: 0.57, 0.50–0.64, p<0.0001). Over 2 years, chronic complications such as osteomalacia and fractures (23,508 patients each) showed no differences. In patients with IBD, no significant differences were observed in acute (2,688 each) or chronic complications (2,541 each) between cohorts. Conclusion Ferric carboxymaltose was linked to higher odds of severe and moderate hypophosphataemia but fewer acute complications than other IV iron formulations. The reasons for these differences remain unclear and warrant further research to understand the relationship between IV iron, hypophosphataemia, and clinical outcomes.