Is Dairy Bad for Gut Health?

Dairy has long been a staple in traditional diets, prized for its high nutrient density, especially its content of bioavailable calcium, protein, saturated fats, and fat-soluble vitamins (A, D, and K2).

Dairy — particularly milk, cheese, and yogurt — can be one of the most metabolically supportive foods available when sourced and prepared correctly. It offers a rare balance of calcium and phosphate, essential for healthy bone formation, thyroid function, and cellular energy production.

In fact, calcium from dairy is more readily absorbed than from most plant sources and is critical for offsetting the bone-wasting effects of stress, which can take calcium from your bones and deposit it into soft tissues — a degenerative process known as tissue calcification.

However, not all dairy is created equal — and not all bodies tolerate it the same.

What to look for when choosing dairy for good gut health

The quality of dairy foods varies greatly, with modern dairy often falling low on the spectrum. 

Ultra-pasteurised, homogenised, grain-fed, and antibiotic-laden milk can be irritating to sensitive or inflamed guts.

Many people with gut damage also lack the lactase enzyme needed to properly break down lactose, making milk and ice cream harder to digest. But this doesn’t mean dairy is inherently problematic — it means that the type and form of dairy matters.

On the high end of the quality spectrum, you’ll find organic, pasture-raised, and preferably non-homogenised or raw milk from healthy cows. These milks maintain their natural enzyme activity and richer nutrient profiles. 

Dairy foods also exist on a scale of digestibility, referring to how easy your body and gut find it to break down and process.

Milk and ice cream are often harder to tolerate, while aged cheeses (like Parmesan), soft cheeses, and fermented dairy like yogurt are generally much easier to digest. This is thanks to fermentation, which breaks down lactose and enhances probiotic content, transforming dairy into a more gut-friendly food.

Importantly, you don’t need to consume dairy to be healthy — but you do need to get calcium, magnesium, and other key minerals from somewhere.

Cutting out dairy without a suitable replacement can contribute to bone density loss, hormonal imbalances, and the progression of age-related calcification. Under chronic stress, the body can quite literally dissolve youthful bone tissue to meet its calcium demands — a process that, left unchecked, accelerates ageing and contributes to soft tissue stiffening, joint pain, and arterial plaque buildup.

Plenty of people switch to a non-dairy mylk in the hopes of solving their gut troubles, without realising that unfortunately many plant-based milk alternatives often contain gut-damaging additives which can worsen their symptoms.

Added ingredients can include seed oils, added sugars and emulsifiers, ingredients which can damage the gut lining contributing to intestinal impermeability, aka ‘leaky gut’.

This damage allows toxins and undigested food particles into your bloodstream where they don’t belong and sends your immune system into overdrive, triggering inflammation, skin flare ups and other gut symptoms. 

When choosing a milk, we recommend full-cream or A2 cow’s milk or A2 cow’s milk, or cold-pressed, minimally processed options from local brands — these retain more natural nutrients, are gentler on digestion, and closer to milk in its pure state.

If opting for a plant-based milk, choose one that’s minimally processed with just a few simple ingredients - almonds, filtered water, sea salt — and always check the nutrition panel. 

Are you canceling out your own calcium?

Calcium and phosphorus work together in the body, but the ratio matters — ideally, you want more calcium than phosphorus in your diet.

Dairy naturally provides a favourable calcium-to-phosphorus ratio, which helps support bone health, regulate parathyroid hormone, and prevent calcium from being pulled out of the bones and into soft tissues.

Many people today consume too much phosphorus relative to calcium, which can disrupt mineral balance and contribute to issues like bone loss, soft tissue calcification, and elevated parathyroid hormone (PTH).

This imbalance often stems from a diet high in muscle meats (use collagen to balance your protein intake), processed foods, soft drinks (especially colas), and grain-based products, all of which are rich in phosphorus but low in calcium.

Without enough calcium to balance this intake, the body may pull calcium from the bones to maintain proper blood levels, weakening skeletal integrity over time. Prioritising calcium-rich foods like dairy, sardines, and cooked or brothed leafy greens helps restore this critical ratio.

Here is a selection of our favourite wholefood sources of calcium, that are easy on the gut. Remember quality matters here:

1. Hard cheeses (e.g. Parmesan, Gruyère, aged cheddar)
2. Milk (especially whole, grass-fed, non-homogenized if possible)
3. Yogurt (plain, full-fat, preferably fermented or Greek-style)
4. Sardines (with bones)
5. Canned salmon (with bones)
6. Collard greens (cooked – one of the few greens with a good calcium absorption rate)
7. Tofu (calcium-set).

The bottom line

The solution isn’t to demonise or universally endorse dairy, but to understand where it fits for you.

If tolerated, it can be a low-risk, highly nutritious part of a metabolic-supportive diet. If not, minerals must be thoughtfully replaced through other sources like shellfish, bone broth, small fish with bones (like sardines), or carefully balanced supplementation.

As with all foods, the key lies in quality, preparation, and listening to your body. Whether you’re drizzling cream into your coffee, enjoying a slice of aged cheese, or sipping on raw milk from a local farmer, the best dairy — like the best health — is about using nature to strengthen and restore the body, not work against it.