Can You Drink Coffee on a Low Histamine Diet?

A Personal and Scientific Look at Coffee, Genes, and Histamine Intolerance

I had my first cup of coffee at just 12 years old — growing up in England, it wasn’t unusual. Back then, it was more of a sweet treat, loaded with cream and sugar. As I got older, coffee became a comforting daily ritual. A warm mug in the morning helped me focus, energized me, and made me feel like I was starting the day right.

When I adopted a low histamine diet to help manage chronic symptoms like skin rashes, psoriasis, digestive distress, and insomnia, I was relieved to see that coffee didn’t appear on most “avoid” lists. So, I kept drinking my usual 2–3 cups each day.

But over time, I noticed a pattern: on days I drank more coffee, especially in the afternoon, my symptoms would flare. My skin would itch more, digestion would act up, and sleep became even more elusive. Still, I didn’t want to give up my coffee.

Eventually, I turned to genomic testing for answers. What I discovered completely shifted the way I think about coffee and histamine. It wasn’t just about whether coffee contained histamine — it was about how my body processed the caffeine, dopamine, and chemical compounds in that beloved brew.

Before we dive into the complexity of histamine and genetics, let’s take a moment to recognize that coffee, in and of itself, isn’t a “bad guy.” In fact, it offers several science-backed health benefits, especially when consumed in moderation.

• Rich in Polyphenols: Coffee is a major source of antioxidants in many diets – chlorogenic acids and caffeic acid. These plant compounds help fight inflammation and support immune health.
• Improves Focus and Energy: The caffeine in coffee stimulates the central nervous system, enhancing mental clarity, memory, and even physical performance.
• Supports Gut Health: Coffee contains melanoidins, prebiotic compounds created during roasting. Gut bacteria can ferment these into short-chain fatty acids like butyrate, which is known to calm inflammation and reduce histamine release in the gut.
• Stimulates Digestion: Coffee's bitter compounds promote bile production, which helps break down fats and absorb fat-soluble vitamins (A, D, E, and K). Bile also plays a major role in gut motility (keeps things moving) and promotes healthy detoxification.
• Encourages Metabolic Balance: Coffee consumption has been shown to stimulate GLP-1 (glucagon-like peptide-1), a hormone that regulates blood sugar, appetite, and metabolism — all of which can indirectly reduce histamine buildup.

So clearly, coffee has some powerful upsides. But there's more to the story if you're dealing with histamine intolerance or chronic inflammation.

Technically, no.

According to the food list, SIGHI (Swiss Interest Group Histamine Intolerance) coffee scores a “1” — which means it’s low in histamine. However, it’s important to understand that just because coffee doesn’t contain histamine doesn’t mean it won’t increase histamine in your body.

For some people, especially those with IBS (Irritable Bowel Syndrome), IBD (Irritable Bowel Disease), or leaky gut, coffee can trigger mast cell activation, leading to the release of histamine.
This is often why someone can feel fine drinking coffee for years and then suddenly develop symptoms like:

• • Itchy skin or hives
  • Psoriasis flare-ups
  • Anxiety or jitteriness
  • Bloating or acid reflux
  • Trouble falling or staying asleep

Let’s look at why this happens.

• CYP1A2: The key gene that breaks down caffeine. If you're a slow metabolizer, caffeine stays in your system longer, which can lead to overstimulation and increased histamine through nervous system activation.
• ADORA2A: This gene controls how sensitive you are to caffeine’s effects. People with certain variants are more likely to feel anxious or experience sleep disruptions — both of which can release more histamine.
• COMT (Catechol-O-Methyltransferase): A gene that has many different functions that helps break down dopamine, which rises after drinking coffee. If COMT is slow, dopamine builds up, which can increase anxiety — and histamine — especially if estrogen is also high (since COMT clears both dopamine and estrogen).
• NAT2: A detox gene involved in clearing coffee’s other chemical compounds. Slow NAT2 activity can lead to a buildup of coffee metabolites that trigger oxidative stress and, in turn, histamine release.

So, even if your CYP1A2 gene makes you a fast caffeine metabolizer, you may still react poorly to coffee if your COMT or NAT2 genes are slow.

• Coffee stimulates stomach acid, gallbladder contraction, and gut motility – all great things if your digestion is strong.
• But if you struggle with IBS, GERD, or leaky gut (intestinal permeability), this stimulation can cause gut irritation, mast cell activation, and histamine spikes.
• If you gallbladder has been removed or is sluggish, bile production can be impaired, making coffee harder to tolerate.

Another issue with coffee is how it's grown and stored. Poorly stored beans can develop mold that produces ochratoxin A — a mycotoxin linked to increased histamine and immune reactions.

Some detox genes, including those that break down caffeine, which are involved in Phase I and II liver detox, also break down mold toxins. If you’re genetically slow at this, mold exposure from coffee can seriously tax your system.

Conventional coffee is also one of the most pesticide-sprayed crops. These chemicals can create oxidative stress, burden detox pathways, and worsen histamine overload.

Tip: Choose a high-quality, organic, mold-tested coffee brand, such as Purity Coffee, which prioritizes both health and sourcing integrity.

It depends. Ask yourself:

Do you get anxious, jittery, or flushed after coffee?
Do you notice worsening skin symptoms or digestion after drinking it?
Is your sleep disrupted if you drink it past noon?

If yes, your body may be struggling to process caffeine, dopamine, or other compounds — even if your genetics haven’t been tested. That’s why many women with histamine issues need to reduce or modify their coffee habit.

Thanks to my genomic testing, I discovered I'm a fast caffeine metabolizer (CYP1A2), but slow at clearing dopamine and detoxing (COMT and NAT2). That means I can enjoy coffee — but only 2 cups in the morning, and only if it's organic and mold-free.

Any more than that, and I feel wired, anxious, and inflamed — the telltale signs of rising histamine.

✅ Choose high-quality, organic, mold-tested brands like Purity Coffee
✅ Limit to 1–2 cups, and drink only in the morning
✅ Try decaf — but only water-processed, as some methods increase mold risk
✅ Avoid coffee machines that may have mold buildup (pour-over or French press is best)
✅ Heal your gut before adding coffee back in
✅ Consider genomic testing to personalize your approach

I'd love to guide you if you are ready to dig deeper into how your genes and nutrition impact your health, from histamine intolerance, gut health, hormone balance, and sleep. Let's design a personalized path that works with your body and your genes that are unique to you.

📚 References – “Can You Drink Coffee on a Low Histamine Diet?”

1. Iriondo-DeHond, A., Uranga, J. A., del Castillo, M. D., & Abalo, R. (2021). Effects of Coffee and Its Components on the Gastrointestinal Tract and the Brain–Gut Axis. Nutrients, 13(1), 88. https://doi.org/10.3390/nu13010088

2. Leitão, A. L. (2019). Occurrence of Ochratoxin A in Coffee: Threats and Solutions — A Mini Review. Beverages, 5(2), 36.https://doi.org/10.3390/beverages5020036

3. Low, J. J. L., Tan, B. J. W., Yi, L.-X., Zhou, Z.-D., & Tan, E.-K. (2024). Genetic Susceptibility to Caffeine Intake and Metabolism: A Systematic Review. Journal of Translational Medicine, 22:961. https://doi.org/10.1186/s12967-024-05737-z

4. González de Llano, D., et al. (2021). Melanoidins from Coffee By-Products and Their Prebiotic Properties: A Review. Foods, 10(3), 556. https://doi.org/10.3390/foods10030556