Morning pain in the toes, along with body aches, can be due to joint stiffness, a vitamin deficiency, or conditions like arthritis that cause inflammation and discomfort. Gentle stretching after waking, staying active, and using a warm compress can help reduce stiffness and pain. Make sure your diet supports bone health, and you stay well hydrated. A doctor may recommend appropriate medications or supplements after identifying the exact cause, so it is better to get evaluated if this keeps happening.