Vegans are most commonly deficient in vitamin B12, with roughly half of all vegans falling below healthy blood levels. But B12 is only the beginning. A fully plant-based diet also creates gaps in omega-3 fatty acids, iodine, iron stores, zinc, selenium, choline, and sometimes vitamin D. Some of these deficiencies develop slowly over months or years, making them easy to miss until symptoms appear.
Vitamin B12: The Most Critical Gap
Vitamin B12 is found almost exclusively in animal products, which makes it the single most important nutrient for vegans to supplement. About 52% of vegans have deficient blood levels (below 156 pmol/L), compared to just 1% of omnivores. Across multiple countries, 50 to 70% of vegans and vegetarians show subnormal B12 status.
What makes B12 deficiency dangerous is how it progresses. Early signs include fatigue and anemia. Over time, low B12 causes neurological damage: cognitive impairment, depression, and in severe cases, dementia-like symptoms. In infants born to deficient mothers, the consequences are even more alarming. Case reports describe babies unable to hold up their heads or grasp objects, with regression in developmental milestones.
Your body can store B12 for several years, so new vegans often feel fine at first. The deficiency creeps in quietly. A 500-microgram B12 supplement taken at least three times per week is enough to maintain healthy levels. Annual blood testing is a reasonable precaution.
Omega-3 Fatty Acids: A Hidden Shortfall
Plant foods provide a type of omega-3 called ALA, found in flaxseeds, chia seeds, and walnuts. But your body needs EPA and DHA, the forms that support brain function and heart health. The human conversion rate from ALA to EPA and DHA is only about 5 to 8%, which is far too low to meet your needs through plant oils alone.
This shows up clearly in blood tests. The omega-3 index, a measure of how much EPA and DHA is in your red blood cells, averages around 2.7 to 3.7% in vegans compared to 5.4% in omnivores. A low omega-3 index is associated with increased cardiovascular risk. Algae-based DHA supplements are the most effective plant-based solution, since algae is where fish get their omega-3s in the first place. The European Food Safety Authority recommends 250 mg per day of combined EPA and DHA.
Iodine: Severely Low Without Dairy or Seafood
Iodine deficiency in vegans is striking. A meta-analysis found that vegans had a median urinary iodine concentration of just 12.2 micrograms per liter, far below the World Health Organization’s optimal range of 100 to 200 micrograms per liter. Average daily iodine intake among vegans was only 17.3 micrograms, a fraction of the recommended 150 micrograms.
In omnivorous diets, dairy products and seafood are the main iodine sources. Without those, vegans rely on seaweed (which varies wildly in iodine content and can actually provide too much) or iodized salt. If you cook mostly from scratch and don’t use iodized salt, your intake could be close to zero. Low iodine impairs thyroid function, leading to fatigue, weight changes, and difficulty concentrating.
Iron: Adequate Intake, Poor Absorption
Vegans often eat plenty of iron-rich foods like lentils, spinach, and beans. The problem is absorption. Plant foods contain only non-heme iron, which your body absorbs less efficiently than the heme iron found in meat. Compounds naturally present in plant foods, including phytates, oxalates, and polyphenols, further block iron uptake.
The result is lower iron stores even when total iron intake looks fine on paper. Studies consistently show that vegans have lower ferritin (your body’s stored iron) than omnivores. In one comparison, male vegans averaged 72 micrograms per liter of ferritin versus 141 in meat eaters. Among women, the gap was similar, with some vegan women averaging just 13.6 micrograms per liter compared to 33.6 in omnivores.
You can improve absorption by pairing iron-rich foods with vitamin C, eating fermented foods like tempeh, and cooking in cast iron. Soaking and sprouting grains and legumes also reduces phytate content, freeing up more iron for absorption.
Zinc: Phytates Are the Problem Again
Zinc absorption follows the same pattern as iron. The phytate in whole grains, legumes, nuts, and seeds binds to zinc and reduces how much your body can use. Modeling research found that adding 1,000 mg of phytate to the diet doubles the amount of zinc you need to eat to meet requirements, and 2,000 mg of phytate triples it. At a phytate-to-zinc ratio above 11:1 for men or 15:1 for women, it becomes nearly impossible to absorb enough zinc regardless of how much you eat.
Vegan diets tend to be high in phytate by default. The same strategies that help with iron, soaking, sprouting, and fermenting, also reduce phytate’s interference with zinc. Pumpkin seeds, chickpeas, and cashews are among the better plant-based zinc sources.
Selenium: It Depends on Where Your Food Grows
Selenium content in plant foods varies dramatically based on the soil where those plants were grown. In a study comparing dietary groups, vegans had a median serum selenium of 52.84 micrograms per liter versus 62.85 in omnivores. Forty percent of vegans fell below the 50 microgram per liter threshold, compared to just 2.5% of omnivores.
Larger dietary surveys found that 33 to 49% of vegans did not reach the recommended selenium intake. A single Brazil nut contains roughly a day’s worth of selenium, but the content varies so much that it’s not a perfectly reliable source. If you live in a region with selenium-poor soil, like parts of Europe and China, the gap is likely wider.
Vitamin D: Not Uniquely a Vegan Problem
Unlike the other nutrients on this list, vitamin D deficiency doesn’t track neatly with vegan diets. A large study of Adventist populations found no significant difference in blood vitamin D levels between vegans, partial vegetarians, and nonvegetarians after adjusting for age and sex. Skin color and sun exposure were far stronger predictors: 58% of Black participants were deficient compared to 15% of white participants, regardless of diet.
That said, vegans tend to have lower vitamin D intake from food because the richest dietary sources are fatty fish, egg yolks, and fortified dairy. Depending on your age, location, and skin tone, a daily supplement of 400 to 2,000 IU may be necessary. Vegans living at high latitudes who don’t use fortified foods or supplements are at the highest risk for low levels and reduced bone density.
Choline: Widely Overlooked
Choline is essential for liver function, brain development, and nerve signaling, yet most people have never heard of it. The richest food sources are eggs, liver, and salmon. Plant sources exist (shiitake mushrooms, wheat germ, Brussels sprouts, almonds) but contribute only about 10% of daily needs per serving. Vegetarians as a group average just 192 mg per day, well below the adequate intake of 425 mg for women and 550 mg for men.
Vegans likely fare worse. Because choline requirements were only formally established in 1998 and public awareness remains low, this nutrient rarely appears on supplement labels or in dietary planning guides for plant-based eaters.
Protein Quality: Amino Acid Gaps
Total protein intake on a vegan diet is usually sufficient. The real issue is amino acid balance. Plant proteins contain less leucine (about 7.1% on average versus 8.8% or higher in animal proteins) and are often low in one or more essential amino acids. Wheat protein, for example, scores just 25% on the standard protein quality scale, largely because it contains only 31% of the lysine your body needs. Legumes like peas and beans are low in sulfur-containing amino acids instead.
The fix is straightforward: eat grains and legumes together. Cereals lack lysine but have adequate sulfur amino acids, while legumes are the reverse. Combining them, rice and beans, hummus and pita, lentil soup with bread, creates a complete amino acid profile. You don’t need to combine them at the same meal, but eating both regularly throughout the day covers your bases.
Practical Priorities
Not all of these deficiencies carry equal urgency. Vitamin B12 is non-negotiable and requires supplementation. Omega-3s from algae, iodine from iodized salt or a supplement, and vitamin D in winter months or northern climates are the next tier. Iron, zinc, selenium, choline, and protein quality can usually be managed through thoughtful food choices: pairing vitamin C with iron-rich meals, soaking grains to reduce phytates, eating Brazil nuts for selenium, and combining legumes with grains for complete protein.
A vegan diet can meet nearly all nutritional needs, but it takes deliberate planning. The nutrients listed here are the ones that won’t take care of themselves.