Starting the Autoimmune Protocol means removing entire food groups to help identify what triggers your symptoms. It's powerful, and for many people it brings real relief. But here's what we don't talk about enough: when you eliminate grains, legumes, dairy, eggs, nuts, seeds, and nightshades, you're also cutting out major sources of vitamins and minerals your body needs.

We've been there. When we created our baking mixes, nutrient density wasn't just a bonus feature. It was the entire point. Most AIP treats rely on coconut flour alone or cassava flour alone, and those single-flour recipes leave gaps. That's why we blend cassava, coconut, and tiger nut flour together. Each one brings vitamins, minerals, and prebiotics that help fill the holes elimination creates.

But even the best baking mixes can't do all the work. If you're following AIP, you need to know which nutrients are at risk and how to get them from whole foods. Let's talk about the big ones and what you can do about them.

Calcium Without Dairy

Dairy provides about 75% of calcium in the typical American diet. When you remove it on AIP, you lose your main calcium source overnight.

Calcium does more than build bones. It keeps your muscles working, your nerves firing, and your heart beating in rhythm. When your diet doesn't provide enough, your body pulls calcium from your bones to keep your blood levels stable. Over time, that can lead to bone loss.

The RDA for calcium is 1,000 mg per day for most adults. Research shows about 40% of adults don't hit that target even with dairy in their diet. On AIP, your risk is higher.

Your best AIP calcium sources are sardines with bones (351 mg per can), canned salmon with bones (about 180 mg per 3 oz), leafy greens like collard greens (268 mg per cup cooked) and kale (94 mg per cup cooked), and bone broth made with apple cider vinegar to pull minerals from the bones.

Here's the key: you need these foods consistently. A serving of collards twice a week doesn't cut it. Think daily leafy greens, bone broth as a staple, and sardines or canned salmon multiple times per week.

Vitamin D: More Than Sunshine

AIP removes eggs and dairy, your two main dietary sources of vitamin D. More than 42% of American adults are deficient in vitamin D even before cutting these foods. On AIP, that risk climbs higher.

Vitamin D matters for immune regulation. It helps your regulatory T cells tell the difference between dangerous invaders and your own healthy cells. When people with autoimmune disease have adequate vitamin D, their immune systems are less likely to attack their own tissues.

AIP food sources include fatty fish like salmon (570 IU per 3 oz), mackerel, and sardines, liver (about 42 IU per 3 oz of beef liver), and UV-exposed mushrooms (some brands contain up to 400 IU per serving).

The problem? Even the best food sources don't get you to optimal levels without serious sun exposure. Most people on AIP need to supplement, especially if you live in a northern climate, work indoors, or have darker skin. Work with your doctor to test your levels and supplement based on your results. Food alone usually isn't enough.

B Vitamins: The Energy Problem

Grains, legumes, and eggs are major B vitamin sources. Remove them, and you lose a lot of nutritional density fast.

Research on women with Hashimoto's following AIP found that 50% had deficiencies in folate, vitamin B12, or riboflavin even while on the protocol. B vitamin deficiencies show up as fatigue, brain fog, mood issues, and neuropathy.

For B12, eat liver and organ meats (60-85 mcg per 3 oz of liver), clams and mussels (84 mcg per 3 oz of clams), and sardines and salmon (about 5 mcg per 3 oz). For folate, focus on liver (290 mcg per 3 oz), leafy greens like spinach (263 mcg per cup cooked), and asparagus (268 mcg per cup cooked).

If you're not eating liver or organ meats regularly, you're at high risk for B12 deficiency. Most people need at least one serving of liver per week. Many benefit from supplementation on top of that.

Potassium: When Nightshades Are Off the Table

Nightshades like tomatoes, potatoes, eggplant, and bell peppers provide a lot of potassium. Remove them, and you lose a significant source of this electrolyte. Low potassium causes muscle cramps, constipation, fatigue, and irregular heartbeat.

The RDA for potassium is 2,600 to 3,400 mg per day depending on age and sex. Most Americans fall short even with nightshades in their diet.

AIP sources include sweet potatoes (542 mg per medium sweet potato), winter squash like acorn or butternut (896 mg per cup cooked), plantains (913 mg per cup cooked), avocado (708 mg per avocado), and leafy greens like Swiss chard (961 mg per cup cooked).

You need potassium-rich foods every single day. Think multiple servings of starchy vegetables, greens, and fruits daily. A sweet potato here and there won't maintain your levels.

Magnesium: No Nuts, No Seeds, No Problem?

Nuts, seeds, legumes, and whole grains are the main dietary sources of magnesium for most people. All eliminated on AIP. Magnesium is involved in over 300 enzymatic reactions in your body, including energy production, muscle and nerve function, and blood sugar regulation.

Magnesium deficiency increases pro-inflammatory cytokines, which raise inflammation. That's exactly what you're trying to avoid.

AIP sources include leafy greens like spinach (157 mg per cup cooked), Swiss chard (150 mg per cup cooked), and kale (31 mg per cup raw), avocado (58 mg per avocado), and bone broth.

Leafy greens need to be a daily staple, not an occasional side dish. You're looking at multiple cups of cooked greens per day to meet your magnesium needs from food alone.

Zinc: The Immune Function Essential

Zinc is critical for immune function, wound healing, and DNA synthesis. The best sources are oysters, red meat, and poultry. While AIP allows these foods, many people don't eat enough animal protein to meet their zinc needs.

Zinc deficiency is common in people with autoimmune disease, especially inflammatory bowel disease, because gut inflammation interferes with absorption. Even if you're eating zinc-rich foods, your body may not be absorbing it efficiently.

AIP sources include oysters (74 mg per 3 oz, the best source by far), red meat like beef (7 mg per 3 oz), lamb, and bison, and poultry like chicken and turkey (2 to 3 mg per 3 oz).

You need animal protein at every meal. If oysters aren't in your regular rotation and you're not eating red meat daily, supplementation may be necessary. Work with your doctor to test your levels.

Fiber: Your Gut Needs This

Whole grains, legumes, nuts, and seeds are primary fiber sources. Remove them, and your fiber intake drops significantly. Fiber feeds your gut microbiome and helps produce anti-inflammatory compounds like butyrate. Without adequate fiber, your gut bacteria can't do their job.

Research shows most people on AIP are fiber-deficient, which is ironic given that gut health is a main reason people start the protocol.

AIP fiber sources include starchy vegetables like sweet potatoes, plantains, and winter squash, non-starchy vegetables like broccoli, Brussels sprouts, and cauliflower, fruits like berries, apples, and pears, and tiger nut flour (very high in prebiotic fiber).

You need a wide variety of vegetables and fruits every single day. If your AIP diet is mostly meat and a small side of vegetables, you're not getting enough fiber. Aim for at least five servings of vegetables per day, plus one to two servings of fruit.

Tiger nut flour is one reason we use it in our baking mixes. It's packed with resistant starch and prebiotic fiber that feeds beneficial gut bacteria. Every bite supports your microbiome.

How to Protect Yourself

Nutrient deficiencies on AIP aren't inevitable, but they're common if you're not intentional.

Eat organ meats at least once per week. Liver is the most nutrient-dense food available. If you can't stand the taste, try pâté or finely ground liver mixed into ground meat.

Prioritize leafy greens every day. Spinach, kale, collard greens, and Swiss chard provide calcium, magnesium, folate, and potassium. Aim for at least one to two cups of cooked greens per day.

Drink bone broth regularly. Made with bones, joints, and apple cider vinegar, it provides calcium, magnesium, and collagen. Use it as a base for soups or drink it straight.

Don't skimp on animal protein. Red meat, poultry, and seafood provide B12, zinc, iron, and quality protein. If you're trying to eat mostly plants on AIP, you will become deficient.

Include fatty fish at least twice per week. Salmon, sardines, mackerel, and anchovies provide vitamin D, omega-3 fatty acids, and calcium (if you eat the bones). Canned fish with bones is one of the best calcium sources on AIP.

Eat the rainbow. Different colored vegetables and fruits provide different nutrients. Don't eat the same five foods every day. Rotate your choices to maximize variety.

Consider supplements strategically. Vitamin D, magnesium, and B12 are the most commonly needed. Work with your doctor to test your levels and supplement what you actually need. Don't just take a handful of pills and hope.

Don't stay in elimination longer than necessary. AIP elimination is a diagnostic tool, not a permanent diet. The longer you stay in elimination, the higher your deficiency risk. Most people should move to reintroduction after 30 to 90 days.

The Real Talk

AIP is powerful for identifying food triggers and reducing inflammation. But it comes with real nutritional risks if you're not paying attention. Calcium, vitamin D, B vitamins, potassium, magnesium, zinc, and fiber are commonly deficient on AIP.

You can prevent deficiencies by eating organ meats, leafy greens, bone broth, fatty fish, and a wide variety of colorful vegetables and fruits every day. Supplementation may be necessary for vitamin D, magnesium, and B12.

If you've been in elimination for months and you're feeling worse instead of better, nutrient deficiency could be why. Work with a healthcare provider who understands the protocol to test your levels.

Our baking mixes help fill some gaps. Tiger nut flour provides prebiotic fiber. Cassava flour provides B vitamins and minerals. Coconut flour adds fiber and healthy fats. We designed these blends to add nutrient density, not just empty calories.

If you're doing AIP, do it right. Pay attention to what you're eating, test your levels, and don't stay in elimination longer than you need to. The goal is healing, not creating new problems.