Whether you choose to take iron supplements in the morning or at night is up to you, however, making yourself a schedule can help prevent you from accidentally skipping a dose. Despite past recommendations to take iron pills with food, recent studies suggest that several types of foods such as coffee and milk can actually interfere with your bodies ability to absorb iron. For this reason, doctors now recommend taking iron pills on an empty stomach with water, usually an hour or so before or after a meal.