I remember sitting in my kitchen, a few months after my celiac diagnosis, still feeling like a wrung-out dishrag. I was doing everything right-no gluten, no dairy, reading every label like a detective. So why did I still need a nap by 10 a.m.? Why were my legs restless at night and my brain foggy during the day? I started digging into the research and talking with my dietitian, and a picture came together: even with a strict gluten-free diet, my body was still playing catch-up on nutrients it had been missing for years.
If you’ve been diagnosed with celiac disease, or you’re a parent managing it in a child, you’ve probably wondered the same thing: what are the actual signs that your body is low on key vitamins and minerals? This post is the deep dive I wish someone had handed me back then. I’m not a doctor, and this is not medical advice-just the notes I took as a mom who wanted to understand what was happening inside and how to spot the clues my body was giving me.
Why celiac disease can create nutrient gaps
Celiac disease doesn’t just cause a reaction to gluten. It flattens the villi-those tiny finger-like projections in your small intestine that grab nutrients from food and shuttle them into your bloodstream. When they’re damaged, you don’t absorb iron, B12, folate, calcium, zinc, and a whole list of other essentials the same way a healthy gut would. Healing takes time, and during that healing (and often even afterward, if you get accidentally glutened or have ongoing low-level inflammation), you can run low on things your body needs to function. That’s why fatigue, brain fog, and a host of other sneaky symptoms can stick around.
I learned that even with a beautifully clean gluten-free diet, some nutrients are harder to get enough of simply because the standard Western plate relies on fortified wheat products. Take away bread, cereal, and pasta, and you’ve taken away the vehicle for a lot of added B vitamins and iron-unless you deliberately replace them.
Common deficiencies and what they feel like
Here’s a rundown of the deficiencies that showed up again and again in my research, along with the signs I learned to recognize in my own household.
Iron
Iron deficiency is a big one in celiac disease, partly because the damage happens right where iron is absorbed (the upper small intestine). The sign I noticed first was an exhaustion that sleep didn’t fix. Other clues:
- Feeling short of breath with light activity
- Looking pale
- Brittle nails with ridges
- Cold hands and feet
- A strange craving to chew ice
In kids, you might see irritability or trouble concentrating in school.
Vitamin B12 and folate
B12 and folate work together to make red blood cells and keep your nervous system humming. When they’re low, the signals can be subtle: a pins-and-needles sensation in your hands or feet, a tongue that feels swollen or smooth, memory slips, and a mood that dips for no clear reason. Because B12 is found mostly in animal foods, and folate in leafy greens and legumes, someone who is also avoiding dairy or eating mostly processed gluten-free replacement foods might miss out.
Vitamin D
Vitamin D is less about digestion and more about overall inflammation and immune function, but many people with celiac have low levels, especially if they live in a northern climate or aren’t out in the sun much. The symptom I hear most often from other moms is bone pain-a deep ache in the shins, hips, or lower back-alongside muscle weakness. In kids, it can show up as slow growth or frequent illness.
Calcium
Calcium absorption suffers when the small intestine is inflamed, and a lot of newly diagnosed people also cut out dairy right away because of lactose intolerance from villi damage. Signs of low calcium can include muscle cramps, a tingly sensation around the mouth or in the fingers, and brittle teeth. Over the long haul, untreated calcium deficiency can chip away at bone density. That’s not something you feel, but it’s a quiet risk worth watching.
Zinc
Zinc is a behind-the-scenes player for your immune system, skin, and wound healing. A deficiency might show up as cracks at the corners of your mouth, slow-healing cuts, hair that’s thinning or falling out more than usual, and a weaker sense of taste or smell. I noticed my kids’ appetites dipped when they were running low, and their colds stuck around longer.
Magnesium
Magnesium seems to be the nutrient people realize they’re missing only when they start getting leg cramps at night or twitching eyelids during the day. Anxiety, insomnia, and a heartbeat that feels fluttery can also be red flags. Because magnesium is eliminated faster when you’re stressed (hello, parenting), it’s easy to burn through your stores.
How to catch them before they catch up with you
The symptoms I listed overlap with, well, just about everything. So self-diagnosing from a blog post is not the move. But keeping a simple symptom log and sharing it with your doctor can be the nudge that leads to lab work. I keep notes on my phone: “Kolbie, tired after school three days in a row, craving ice,” or “Me, weird eye twitch back again.” When I brought those notes to our doctor, we discovered Kolbie was low in ferritin (her iron stores) and I was scraping the bottom on magnesium.
Routine labs after a celiac diagnosis typically include a complete blood count, iron panel, vitamin D, B12, and folate. If you’re not getting better after going gluten-free, asking your care team to check zinc and magnesium is a reasonable step, too. And if you’re a parent, trust your gut when something feels off. A kid who suddenly hates playing outside or is melting down at homework time might not be defiant-they might be exhausted or foggy.
What this looks like in our everyday meals
I’m not going to hand you a supplement protocol because that’s firmly in “talk to your doctor” territory. But I can share how I approach food with nutrient density in mind, and how Clean Monday Meals products fit into that picture around our house.
The first thing I do is pile the plate with whole, unprocessed ingredients-the kind you can picture in their original form. Dark leafy greens for folate and calcium, red meat and lentils for iron, eggs and fish for B12 and vitamin D, pumpkin seeds and good-quality dark chocolate for magnesium and zinc. Then I build flavor without fillers. That’s where our seasonings and bouillons come in. I use the Chicken Bouillon in everything from pan sauces to rice pilaf because it adds a deep, savory richness without the MSG, seed oils, or mystery additives you find in many conventional grocery store bouillons. It’s low sodium, too, so I’m not overshooting while trying to make dinner taste good. A teaspoon of that in a quick soup or a skillet meal means my family eats the greens because they actually taste delicious, not because I told them to.
When I need iron-rich food to actually make it into my daughter’s mouth, the Beef Ramen Seasoning gets a workout. I’ll brown ground beef with it and stir in shredded zucchini and spinach. She eats the whole bowl, no interrogation required. For a bone-building boost, I make a creamy mushroom pasta sauce using the Cream of Mushroom Soup Mix (dairy-free, soy-free) and stir in wilted kale or chard. The mix gives it a comforting, from-scratch flavor without the work of a roux, so I’m more likely to make it even on a Wednesday. Small strategies like that keep us on top of nutrients without making mealtime feel like a clinical intervention.
Trust the process-and your body
If you’ve just been diagnosed, or you’ve been gluten-free for a while and still feel run down, please know that’s a real thing and you’re not failing. Healing isn’t linear. Your intestinal villi can take months to fully recover, and your nutrient stores might need time to rebuild with food and, if your doctor recommends them, supplements. I’ve had seasons where I felt great and seasons where I bottomed out again after a cross-contact incident, and each time I had to remind myself: this body is working hard, and I can support it with what I put on my plate.
When you cook from scratch with foods you recognize, you take back a lot of control that celiac disease tries to steal. And having a set of clean, allergy-friendly flavor boosters in your pantry makes that habit so much more sustainable. I built Clean Monday Meals exactly for that reason: so our family could eat comforting, normal meals without compromising on safety or nutrition. The more we share and support each other, the more we all thrive.
If you want more recipes that put nutrient-dense ingredients at the center (without a single boring salad in sight), hop over to our free Recipe App. I built it with Chef Cayt to make gluten- and dairy-free cooking feel doable, not overwhelming. Let’s keep taking care of ourselves, one meal at a time.
Anyone else notice a specific symptom that tipped you off to a deficiency? I’d love to hear your story in the comments, and be sure to tag @cleanmondaymeals if you make any of your own nutrient-rich creations.