Yes, our bodies naturally seek homeostasis and healing if we feed ourselves well. Interesting, I’ve also basically cut out coffee from my life, but I find cacao to be medicinal. I think it’s also about dosage and related to your holistic picture of health. Many studies on coffee for example have diverse and even conflicting findings.
There is much research that says that some coffee is good for you, and other research that has disputed that coffee can cause adds a fatigue. From my personal experience, and from what I’ve read according to many sleep experts, caffeine can greatly disrupt the body’s natural circadian rhythm, so you want to be careful and conscious with how much and when you consume, if at all.