Top 6 Nutrition Deficiencies in Celiac Disease and How to Prevent Them on a Gluten-Free Diet

You’ve ditched gluten, cleaned out your kitchen, and probably have a PhD in label reading by now. But even after fully committing to your gluten-free lifestyle, you might be feeling a little… off. Low energy? Slow recovery? Brain fog? Been there, done that. That might not be gluten sneaking in anymore – it could be nutrient deficiencies.

And here’s the deal: they can happen even if you’re eating clean.

Why nutrient deficiencies happen in celiac disease

There are two main reasons why celiacs often struggle with low levels of key nutrients:

1. Malabsorption – Celiac disease damages the small intestine, making it harder for your body to absorb nutrients properly. Even if you’re eating a whole damn rainbow, your gut might not be soaking it all in – especially in the early healing stages.
2. Nutrient-poor GFD (gluten-free diet) – Many gluten-free packaged foods lack the vitamins and minerals found in their wheat-filled original (if we skip the fact that they taste just… ugh). You could be full but still running on empty.

Now that you know, let me show you ways to fix it – or avoid in the best case – based on my experience. Let’s dive into some of the most important nutrients most commonly missing in celiacs and gluten-free athletes – and tips on how to bring them back into play.

Most common deficiencies to watch out for

1. Iron – the energy transporter

Why it matters: Iron helps your blood deliver oxygen to your muscles and brain. Low iron = fatigue, poor endurance, and the dreaded afternoon crash.

Why celiacs are at risk: The upper part of the small intestine (iron absorption zone) is often the most damaged.

Fuel fix:

• Load up on lentils, leafy greens, tofu, lean meats, and dried fruit.
• Pair iron foods with vitamin C for better absorption (think spinach + potatoes).
• My personal go-to: Red fruit juice from Amecke or hohes C with added iron – Mix 2:1 with sparkling water and rehydrate post-training. Thank me later.

2. Vitamin B12 – the brain & nerve defender

Why it matters: B12 supports nerve health, energy, and red blood cell formation – all key for performance and focus.

Why celiacs are at risk: Inflammation or coexisting conditions can block the B12 uptake.

Fuel fix:

• Consider eggs, meat, dairy or fish.
• Sauerkraut and other fermented foods like tempeh, as well as fortified plant-based alternatives, might be the option if you are vegan or vegetarian. If this is your case, you might be at risk. Get check-ups regularly and supplement if needed.

3. Vitamin D & calcium – the bone-building duo

Why it matters: Vitamin D helps you absorb calcium, and both are crucial for strong bones and injury prevention – especially important if you’re training hard.

Why celiacs are at risk: Damaged intestines don’t absorb these well, and most gluten-free and lactose-free diets lack enough fortified sources.

Fuel fix:

• Soak up some sun – at least 20 mins a day on your face and arms is a common recommendation
• Eat fatty fish, egg yolks and milk products
• Great veggie sources are leafy greens (kale), almonds, white beans and tempeh.

4. Magnesium – the muscle recovery master

Why it matters: Magnesium supports muscle function, nerve health, and energy production. Low levels = cramps, irritability, and, again, fatigue.

Why celiacs are at risk: Poor absorption + low magnesium in many gluten-free products = deficiency risk.

Fuel fix:

• Munch on nuts, seeds, avocados, and dark leafy greens.
• Fruits like berries or oranges with dark chocolate are the perfect snack if you ask me
• I love my 100% raw cocoa powder with hot almond milk before bedtime (add some collagen for that extra recovery boost).

5. Folate (Vitamin B9) – the cell repair king

Why it matters: Folate supports red blood cell production and helps your body repair tissue post-workout. It’s also linked to mood and cognitive function.

Why celiacs are at risk: Damaged intestines = poor folate absorption, and many gluten-free flours aren’t enriched.

Fuel fix:

• Go for dark leafy greens, citrus, bananas, beetroot and variety of nuts & seeds.
• Broccoli and Brussels sprouts as well as beans, lentils, and peas – maybe just not before training 😉

6. Zinc – the immune booster

Why it matters: Zinc helps with immune function, tissue repair, and muscle building. It’s key for staying healthy and bouncing back faster.

Why celiacs are at risk: Zinc is absorbed in the small intestine – and yep, celiac damage strikes again.

Fuel Fix:

• Add zinc-rich foods like poultry, red meat, dairy and eggs
• Plant-based sources are seeds (hemp, pumpkin), quinoa, brown rice and legumes
• If you’re a fan of seafood, go for lobster, shellfish, crab, or, if you dare, oysters (I warned you).

But I’m eating healthy! Why am I still low?

Here’s the truth: even if you’re tracking all your macros and making healthy choices, your gut may still be running behind. Healing takes time. And unless you’re super intentional about nutrient variety, your gluten-free diet might be missing key players. If the symptoms persist, consult your doctor about blood testing and the possible need to supplement.

The G-free Athlete’s power moves

Here’s how to stay fueled and strong on your gluten-free daily basis:

• Choose whole, nutrient-dense foods over ultra-processed GF alternatives
• Get regular blood work (ask for iron, B12, vitamin D, folate, and zinc)
• Supplement smartly – don’t DIY; consult with your doctor, test first, then take. It makes no sense to jump into supplementing unless there is a specific need behind it.
• Find fortified products that add back iron, B vitamins, and more – juices, milk etc.

Work with a pro – especially one who gets the gluten-free athlete lifestyle 😉

Celiac disease might have changed your lifestyle, but it doesn’t get the last word. With the right nutrient strategy, you can fuel smarter, recover faster, and perform at your very best. Get your gut back in the game!

Sources:

Caruso R, Pallone F, Stasi E, Romeo S, Monteleone G. Appropriate nutrient supplementation in celiac disease. Ann Med. 2013

Theethira TG, Dennis M, Leffler DA. Nutritional consequences of celiac disease and the gluten-free diet. Expert Rev Gastroenterol Hepatol. 2014

Malterre T. Digestive and nutritional considerations in celiac disease: could supplementation help? Altern Med Rev. 2009

Melinda Dennis, MS, RD, LDN, Lauren Alder Dear and Lindsey O’Regan. Common Nutrient Deficiencies in People with Newly Diagnosed/Untreated Celiac Disease

Dennis M, Kupper C, Lee AR, Sharrett MK, Thompson T. Celiac Disease Toolkit. American Dietetic Association, 2011