Nutritional Deficiencies in IBD and IBS: Nutrients to Improve Gut Health

From scientific research and clinical practice with hundreds of patients, individuals with inflammatory bowel disease (IBD) (and many with irritable bowel syndrome – IBS) often struggle with vitamin and mineral gaps. In IBD, dysbiosis, inflammation, and increased intestinal permeability reduce absorption just when needs are higher. In IBS, persistent symptoms and cautious restriction quietly erode intake. Because many of these nutrients are essential, a targeted plan with supplements when absorption is low, and anti-inflammatory foods as the gut heals is often what works best.

During active inflammation or malabsorption, nutrient absorption is often very low, so some specific supplements are commonly needed. As we repair the gut lining and rebalance the microbiota, absorption improves and food can do more of the heavy lifting again.

Supplements That Move The Needle

Always personalise according to labs, medications, body size, pregnancy, kidney/liver status, and tolerance.

Iron: Use when ferritin/TSAT are low or anemia is present. If oral forms aggravate the gut or don’t work, intravenous iron is often appropriate in IBD flares. If oral is used, pick gentler forms (e.g. bisglycinate, liposomal iron), separate from calcium, tea and/or coffee, and add vitamin C if tolerated.
Vitamin D: Commonly low in IBD and not rare in IBS. Replete to sufficiency and consider pairing with vitamin K2 and adequate calcium in bone-risk patients.
Vitamin B12 & Folate (B9): B12 risk rises with ileal disease/resections, long-term PPI use, low stomach acid, vegan diets; folate needs climb with methotrexate/sulfasalazine or low intake. Even without frank deficiency, a short, supervised course of activated B-complex (methylcobalamin + 5-MTHF) can support energy, nervous-system function, methylation/detox pathways.
Zinc: Very commonly low in IBD and can be suboptimal in IBS-D. Supports tight-junctions and mucosal repair. When using zinc (better bisglycinate or citrate) beyond 8-12 weeks or at higher doses, monitor copper or co-supplement small amounts to avoid copper-deficiency anemia/neuropathy.
Vitamin A / Retinol: Consider clinician-supervised courses when intake is poor and barrier symptoms persist. Avoid taking high doses during pregnancy or if you’re trying to conceive. Do not substitute with beta-carotene, as it does not have the same therapeutic effect.
Selenium: Consider when deficiency is documented (post-resection, very restricted diets). Use modest, time-limited dosing – more is not better.
Magnesium: Losses rise with diarrhoea/high output. Choose bisglycinate or topical oil if stools are loose (gentler than osmotic forms).
Calcium: Often needed alongside vitamin D/K2 in patients with steroid exposure, low intake, or low BMD. DEXA guides bone strategy. In this case, prefer foods like green vegetable broth, juice, almond or tahini if tolerated.
Electrolytes (Sodium & Potassium): With diarrhoea/ileostomy, targeted oral rehydration and potassium repletion can be important. Start with small and well-tolerated doses, especially if you have loose stools.
Omega-3: Not a stand-alone strategy for maintaining IBD remission, but it can support a calmer inflammatory milieu and cardiometabolic health when tolerated.

Anti-Inflammatory Foods That Supply These Nutrients

During active symptoms, keep textures soft: cooked, peeled, blended, and eat small portions. Exclude legumes, cocoa, spicy foods, dairy and gluten grains, especially during the first phase. Other foods like some vegetables, fruits, nuts, shellfish depend on personal tolerances, so if you have problems maintaining a balanced diet, contact an expert dietitian or nutritionist.

Small oily fish: Fish like sardines, anchovies, mackerel (canned in olive oil if tolerated) are a good source of natural iron, vitamin D, selenium, omega-3, and vitamin A (some varieties).
Eggs: Rich in vitamins B12, A and D, and choline. Eggs are also an easy protein vehicle for low-fiber meals.
Lean poultry & slow-cooked meats: Gentle heme iron and vitamin B12 sources when shredded or well-chewed.
Cooked green vegetables: Sources of vitamin A, C, and potassium. Lower fibre load when blended.
Low-acid fruit: Ripe bananas, papayas and melons are rich in vitamin C and potassium.
Tolerated gluten-free starches: White rice, rice flakes or pasta, potatoes and sweet potatoes are energy carriers while the gut settles.
Extra-virgin olive oil: Core anti-inflammatory fat, improves carotenoid absorption from cooked vegetables.

Later on, if you’re gut is stable, you may reintroduce other foods:

Shellfish: Mussels, oysters and clams are rich in nutrients like zinc, vitamin B12, iron, copper and selenium.
Fermented foods: Slowly introduce foods like yogurt and/or kefir if well-tolerated. Add probiotics for later phases.

Add cautiously, one at a time, with professional guidance.

What About IBS?

IBS is functional, and even though it is not considered an inflammatory condition and does not cause ulcers in the gut mucosa, it is often triggered by gut dysbiosis and leaky gut condition. In addition to that, months of symptom-driven restriction can create quiet deficiencies. Consider B12/folate checks in IBS with stomach problems, low stomach acid, long-term PPI (proton pump inhibitors) use, vegan patterns, prior bariatric surgery, or suspected MTHFR variants (in this case prefer 5-MTHF instead of classic B12 and folic acid). In IBS-D (with diarrhoea) or highly restricted eaters, zinc support (with copper awareness) and vitamin D may help barrier function – always individualised.

Putting It Into Practice: How We Phase the Work

Stabilise With Supplements

Start where absorption is: correct identified deficiencies and, when clinically appropriate, use strategic support even without clear deficits (e.g., activated B12/5-MTHF for detox pathways, zinc/retinol for permeability). Do this with professional supervision to avoid interactions or excess.

Eat to Calm, Then to Nourish

While symptoms are active, follow the anti-inflammatory, low-irritant list above (no legumes, cocoa, A1 casein or gluten grains, and introduce shellfish later). Use texture and portion control to lower symptom risk. As the mucosa settles, reintroduce nutrient-dense foods methodically and diversify.

Repair the Gut with the 5R method

Remove triggers (problem foods, alcohol excess, and treat infections if present).
Replace digestive support (acid, enzymes, bile aids if indicated).
Repair the mucosa (zinc, vitamin A, sleep, quality diet).
Reinoculate with beneficial microbes (fermented foods as tolerated, evidence-based probiotics if appropriate).
Rebalance lifestyle (fibre progression, movement, stress regulation, circadian rhythm.

Conclusion

In both IBD and IBS, beginning with supplements during low-absorption phases and then leaning into a calming, anti-inflammatory plate is a practical, patient-friendly way to restore status. With professional guidance including smart choices like activated B12/folate for detox support and zinc/vitamin A for permeability, patients can move through the 5R steps, widen variety, and rely on food again. That’s how we turn nutrition science into better energy, resilience, and quality of life.

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References:

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Frequent Nutritional Deficiencies in IBD and IBS: Micronutrients to Improve Gut Health

Supplements That Move The Needle