Keeping your coffee black, organic, and limited to one cup per day helps to limit the negative effects of coffee (Link). Also, since coffee can reduce iron absorption during meals, many doctors suggest drinking coffee an hour after, or before, your meals.
Dr. Oz puts it well: "Don’t let coffee or [black] tea scare you! They both have multiple health benefits, so you shouldn’t avoid drinking them. In fact, even if you drink tea or coffee with your meals, if you’re not already anemic, chances are you’re getting the iron you need anyway. If you’re constantly fatigued and think you may have iron-deficiency anemia, you should see a doctor and get your iron levels tested" (Link).
1) Iron Deficiency - One study demonstrated that coffee reduced non-heme iron absorption by 39% (Link). Also, iron deficiency is linked with hair loss. "A review of 40 years of research shows that iron deficiency has a much closer link to hair loss than most doctors realize. It may be the key to restoring hair growth, Cleveland Clinic dermatologists find" (Link).
Black tea was also included in this study, and has similar results. "Black tea, and even coffee to a lesser extent, also block iron absorption" (Link). However, cultures that drink green tea do not suffer from anemia more than other cultures (Link). In fact green tea has been proven to regrow hair on mice (Link).
2) Adrenal Fatigue - It is well known that adrenal fatigue and stress can lead to hair loss. But can coffee can lead to adrenal fatigue? "What happens over time is that your adrenal glands start to burn out from overuse, which can lead to adrenal fatigue. Naturally, you can help to prevent adrenal fatigue simply by avoiding coffee, or keeping your consumption to a minimum" (Link).
3) B Vitamins - "Caffeine also reduces the levels of vitamin B which is necessary for healthy hair." (Link)
"I decided to stop drinking coffee. Was very hard in the beginning...but I did it and all my problems are gone! My hair stopped falling almost completely and is more strong now." (Link)