Vitamin B12 deficiency can cause symptoms like headaches, fatigue, depressive mood, gastrointestinal issues, and more. While vegetarians are at a higher risk of vitamin B12 deficiency, it can affect non vegetarians too. Check Headache After B12 Shot: 3 Effective Strategies to Feel Better The Weird Connection Between B12 Deficiency & Migraine Headaches Experiencing any of these symptoms? B12 supplementation might be right for you. Some causes of low B12 are diet, alcohol use, certain diseases like Chrohn's and Celiac Disease, and Gastric Bypass surgery,