Most of the iron in an iron tablet is never absorbed. The rest travels on through your gut, where it can irritate the lining and feed some of the less helpful bacteria living there. That is why iron so often causes constipation, nausea and stomach upset, and why it turns stools a harmless dark colour. None of it is a reason to stop iron that has been prescribed for you. This guide explains what iron does inside your gut, what the research shows about your gut bacteria, and how to make a course easier to live with.
What do iron supplements do to your gut?
The iron tablet most people in the UK are prescribed is ferrous sulfate. Ferrous fumarate and ferrous gluconate are the usual alternatives, and NICE guidance for GPs lists all three as first-line choices. Each delivers a form of iron the gut can absorb, and that form is chemically reactive. A concentrated dose sitting in the stomach and upper intestine can irritate the lining directly.
That irritation has been measured. A large review of placebo-controlled trials found that people taking ferrous sulfate had more than double the odds of gut side effects compared with people taking a placebo. The usual complaints are constipation, nausea, stomach pain, a metallic taste and, in some people, diarrhoea.
Side effects are the main reason people stop taking iron before their levels have recovered, and stopping early leaves the deficiency untreated. If the tablets are making you miserable, tell your GP or pharmacist. A course can usually be adjusted without being abandoned.
Direct irritation is only the first part of what iron does in the gut. The rest depends on the iron your body never absorbs, which is most of each dose.
Where does the iron you do not absorb go?
Your body has no way to get rid of excess iron, so it strictly limits how much it takes in. A hormone called hepcidin controls absorption in the small intestine, and it keeps the gate mostly closed. In a Swiss study of young women with low iron stores, only around one part in six of a standard dose was absorbed, and taking more iron did not mean absorbing much more.
Everything unabsorbed carries on into the large intestine, home to the trillions of bacteria that make up your gut microbiome. Iron is a resource those bacteria compete for, and they are not equally good at getting hold of it. A detailed review of the microbiology sets out the pattern. Potentially harmful species, including Escherichia coli and Salmonella, are well equipped to scavenge iron and tend to thrive when more of it arrives. Some of the most beneficial groups, including Bifidobacterium, need very little iron and gain nothing from the surplus.
In principle, a regular surplus of iron in the colon feeds the wrong bacteria. That is what the chemistry predicts. What actually happens in people is a separate question, and the studies below give a more mixed answer.
Do iron supplements change your gut bacteria?
Studies in adults point in different directions, and who was studied explains most of the disagreement.
The clearest changes are seen in people whose gut is already inflamed. A randomised trial in people with Crohn's disease or ulcerative colitis treated iron deficiency with either tablets or an infusion into a vein. Both corrected the deficiency, but only the tablets shifted the gut bacteria, and people with Crohn's disease were affected most. A UK study of patients treated for iron deficiency anaemia found that short-chain fatty acids, the helpful compounds gut bacteria make when they ferment fibre, fell after a course of tablets. That study had no comparison group. It shows a change after the course, not proof that the iron caused the change.
In healthy people, changes are much harder to find. An Australian randomised trial gave healthy women iron tablets or a placebo for three weeks and found no difference in their gut bacteria at all. A Canadian study found that women who regularly took high-dose iron carried more of the iron-scavenging bacteria than women taking low doses or none. Women who choose high-dose supplements often differ from women who do not, though. They may eat differently, or be treating a health problem. So the iron itself may not be the cause.
The newest evidence suggests the dose matters. In early 2026, a small Swiss randomised trial compared a low-dose and a standard-dose course in women with low iron. The two doses changed the gut bacteria in different ways, and the standard dose was far harder to live with. Gut side effects were reported by 87% of the standard-dose group and 7% of the low-dose group. It is one small, early trial. Its findings need repeating before firm conclusions are drawn.
So iron supplements can shift the balance of your gut bacteria. The shift is most likely where the gut is already inflamed and at higher doses, and a healthy gut on a short course may show no measurable change at all. Our guide to the signs of an imbalance in your gut bacteria covers what an unsettled balance can look like in daily life. Iron sits alongside antibiotics and acid-reducing medicines on the short list of everyday medicines with a measurable effect on gut bacteria, and each behaves differently.
Do iron supplements cause constipation?
Yes. Constipation is one of the most reported side effects of oral iron, and the NHS page on ferrous sulfate lists it among the common ones. Why iron constipates is less settled than the fact that it does. The unabsorbed iron moving through the bowel is thought to slow things down in more than one way. It irritates the gut directly, it changes how the bowel muscles move, and it shifts the gut bacteria that help govern both. If constipation was part of your life before the tablets, iron tends to make it more stubborn.
What helps is the same as for constipation from any cause. More fibre spread across the week, plenty of fluid, and regular movement, none of which stops the iron doing its job. Our guide to why constipation happens and what helps covers all of this, including the trial evidence on fibre and kiwifruit.
One effect of iron needs separating from a warning sign. Iron turns stools dark grey or black, and on its own that is normal and harmless. The stools that need a same-day call to a GP are black and tarry with an unusually offensive smell, or contain visible blood, because those can be signs of bleeding in the gut. The red flags at the end of this page cover this in full.
Can a test show what iron has done to your gut?
Partly. A stool test cannot see irritation of the stomach or gut lining, cannot tell you whether iron caused what it finds, and does not diagnose any condition. It also cannot measure your iron levels. That is a blood test, arranged by your GP.
What a stool test reads is the bacterial side of the story. It shows which groups of bacteria you carry and at what levels, including Bifidobacterium and the fibre-fermenting species that produce short-chain fatty acids. If you have been on iron for months and want to know how your gut bacteria are doing, a gut microbiome test measures the balance of bacteria in a single posted sample, and the result gives you something specific to discuss with a clinician. If constipation is the part you most want answers on, our page on gut microbiome testing for ongoing constipation explains what a result can and cannot tell you.
Why are some people told to take iron every other day?
Hepcidin, the hormone that rations iron absorption, stays raised for about a day after each dose. A tablet taken every day arrives while the gate is still half closed. In a Swiss randomised study of women with low iron stores, those given their tablets on alternate days absorbed about a third more iron overall than those given the same tablets daily.
A larger randomised trial then tested what this means in practice. Women with low iron stores took the same total amount of iron either daily or on alternate days. Iron stores ended up the same in both groups. The alternate-day group reported roughly a third fewer gut side effects on the days they took iron, and fewer of them had slipped back into deficiency six months later. UK guidance for prescribers now includes alternate-day dosing among the options where daily iron is not tolerated.
This is not an instruction to change your own schedule. Both trials were in women with low iron stores rather than diagnosed anaemia, and the right dosing for you depends on how low your levels are and why. If daily iron is treating you badly, raise alternate-day dosing with your GP or pharmacist. Changing a prescribed course on your own risks leaving the deficiency undertreated.
How can you make iron easier on your gut?
None of the following involves stopping your iron:
- Take the course exactly as prescribed, for as long as prescribed. Iron is usually continued for a while after blood levels recover, to rebuild the body's stores, so stopping the moment you feel better undoes part of the treatment
- If the tablets upset your stomach, ask your pharmacist about taking them with or just after a little food. Food reduces how much iron is absorbed, so this is a trade-off to weigh with a pharmacist rather than a habit to adopt quietly
- There is no need to buy vitamin C to take alongside your iron. A randomised trial in adults with iron deficiency anaemia found that iron alone restored blood counts just as well as iron plus vitamin C
- Tea and coffee reduce iron absorption. Leave a gap between them and your tablet. The NHS advises this on the ferrous sulfate page linked above
- Check you are not doubling up. Some multivitamins and pregnancy supplements contain iron, and two sources at once means more unabsorbed iron reaching your gut bacteria
- Keep iron tablets out of the sight and reach of children. Iron overdose is one of the most dangerous accidental poisonings in young children, and a small number of adult tablets can cause serious harm
- Do not start iron on your own because you feel tired. Tiredness has many causes, iron levels are a blood test away, and iron you do not need brings the gut side effects with none of the benefit
- Feed the helpful bacteria. Bifidobacteria and the other fibre-fermenting groups run on plant fibre rather than iron, so a varied, plant-rich diet supports them whatever dose you are on
When should you see a GP?
Iron deficiency itself always deserves a cause. In adults it is often low intake or heavy periods, but it can be the first sign of slow blood loss in the gut. That is why GPs investigate rather than simply prescribing tablets, and why the follow-up appointments matter even when you feel fine. Everyday anti-inflammatory painkillers are one overlooked source of slow blood loss, and our guide to how NSAIDs affect the stomach and gut explains how that happens. Go back sooner if you feel no less tired after a few weeks on the tablets. Iron that is not helping needs reviewing, not persevering with.
While you are taking iron, the following need a GP, or NHS 111 while the surgery is shut:
- Black, tarry stools with an offensive smell, vomiting blood, or vomit that looks like coffee grounds. Iron makes stools dark, but tarry stools and vomited blood need assessing the same day. Call 999 or go to A&E
- Fresh red blood in your stool, or bleeding from your bottom
- Constipation with severe pain, vomiting, or a swollen abdomen
- A change in bowel habit that lasts more than three weeks, or weight loss you cannot explain
- Difficulty swallowing, or vomiting that will not settle
- Worsening tiredness, breathlessness or paleness despite taking your iron, which can mean the anaemia is not responding and needs review
- Digestive symptoms arriving for the first time after 50, or bowel or ovarian cancer in your family
If a child swallows iron tablets, call 999 or go to A&E immediately, even if they seem well. If you are pregnant, check any change to supplements, including iron bought over the counter, with your midwife or GP first.
This guide is for information only and does not replace medical advice. Speak to your GP or pharmacist about your own treatment.
Sources
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- Kortman GAM, et al. (2014). Nutritional iron turned inside out: intestinal stress from a gut microbial perspective. FEMS Microbiology Reviews. PubMed | DOI
- Lee T, et al. (2017). Oral versus intravenous iron replacement therapy distinctly alters the gut microbiota and metabolome in patients with IBD. Gut. PubMed | DOI
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- Ahmed A, et al. (2020). Using volatile organic compounds to investigate the effect of oral iron supplementation on the human intestinal metabolome. Molecules. PubMed | DOI
- Li N, et al. (2020). The efficacy and safety of vitamin C for iron supplementation in adult patients with iron deficiency anemia: a randomized clinical trial. JAMA Network Open. PubMed | DOI
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