What happens to your body when you cut out gluten and dairy?

November 25, 2025 •

5 min read

According to the National Institutes of Health, a gluten-free diet may modify the composition and immune function of the gut microbiota. This major internal change is just one of many that can occur. So, what happens to your body when you cut out gluten and dairy, and is this diet change right for you?

Quick Summary

Eliminating gluten and dairy can significantly reduce inflammation and improve digestive symptoms like bloating and fatigue for sensitive individuals. The diet can also impact energy levels, skin health, and gut microbiome diversity, but requires careful planning to avoid potential nutrient deficiencies.

Key Points

Digestive Improvement: Eliminating gluten and dairy can significantly reduce symptoms like bloating, gas, and abdominal pain, particularly for those with sensitivities or intolerances.
Reduced Inflammation: For many, cutting out these food groups leads to a noticeable decrease in body-wide inflammation, which can alleviate joint pain and fatigue.
Nutrient Awareness is Key: A poorly planned gluten-free and dairy-free diet can lead to deficiencies in essential nutrients like calcium, vitamin D, and fiber.
Focus on Whole Foods: The greatest benefits are seen when processed replacements are avoided in favor of naturally gluten- and dairy-free whole foods such as fruits, vegetables, lean proteins, and legumes.
Consultation is Recommended: Professional medical guidance is important before starting, especially to rule out underlying conditions and ensure nutritional completeness.
Variable Results: The impact of the diet is highly individual; some people experience a dramatic improvement in well-being, while others may notice little difference.
Gut Microbiome Alterations: The diet can change the balance of bacteria in your gut, which requires conscious effort to maintain a healthy and diverse microbiome.

The Initial Adjustment Period: What to Expect

Switching to a gluten-free and dairy-free diet doesn't always lead to immediate improvements. Many people experience a transitional phase, which can be challenging. During this time, the body is adjusting to the removal of familiar foods and the potential decrease in fiber. Some individuals report a temporary increase in headaches, nausea, or fatigue, often referred to as 'withdrawal' symptoms, though scientific evidence for this is limited. These symptoms usually subside within a few weeks as your body adapts to the new dietary patterns. Staying hydrated and focusing on nutrient-dense, whole foods can help mitigate discomfort during this phase. Planning meals and snacks ahead of time is also critical to prevent feeling overly hungry or relying on processed, less healthy alternatives.

The Benefits for Your Digestive System

For those with sensitivities or intolerances, one of the most profound effects of cutting out gluten and dairy is the improvement in digestive health. The body’s digestive system may work harder to process these foods in sensitive individuals, leading to a range of issues.

Gut Lining and Inflammation

Celiac Disease: For individuals with celiac disease, a gluten-free diet is essential. Gluten triggers an autoimmune response that damages the small intestine's lining. Removing gluten allows the gut to heal, improving nutrient absorption and reducing inflammation.
Lactose Intolerance: Those with lactose intolerance lack the enzyme lactase to properly digest lactose, the sugar in dairy. Removing dairy alleviates symptoms like bloating, gas, cramps, and diarrhea.
Non-Celiac Gluten Sensitivity (NCGS): Even without celiac disease, some people experience digestive discomfort from gluten. Removing it can lead to relief from bloating, abdominal pain, and fatigue.

Improved Nutrient Absorption

When inflammation and gut damage from sensitivities are reduced, the intestinal lining can begin to repair itself. A healthy gut is more efficient at absorbing vitamins and minerals from the food you eat. This can combat nutrient deficiencies and boost overall health.

Impact on Inflammation, Energy, and Skin

Beyond digestion, eliminating gluten and dairy can have wider systemic effects. Many people report feeling more energetic and less sluggish, which is often linked to a decrease in overall body inflammation. Some with autoimmune conditions like rheumatoid arthritis or fibromyalgia also find relief from joint pain when removing these foods. For some, dairy, in particular, has been associated with skin issues like acne, due to hormones present in milk. Eliminating dairy can lead to clearer skin and a more vibrant complexion for these individuals.

Potential Pitfalls and Nutritional Deficiencies

While many tout the benefits, cutting out gluten and dairy is not without potential risks, especially if not managed correctly. It is crucial to replace removed food sources with equally nutritious alternatives.

Nutritional Deficiencies

Removing dairy without an alternative plan can lead to deficiencies in vital nutrients such as calcium, vitamin D, potassium, and magnesium. Similarly, cutting out fortified wheat products can result in lower intake of B vitamins, iron, and fiber. It is important to find new sources for these nutrients.

Reliance on Processed Foods

Many gluten-free and dairy-free processed products, such as bread, pastries, and snack foods, are often high in sugar, sodium, and unhealthy fats to compensate for texture and flavor. Over-relying on these alternatives can lead to weight gain and other health problems, negating the potential benefits of the diet. The goal should be to focus on whole, naturally gluten-free and dairy-free foods like fruits, vegetables, lean proteins, nuts, seeds, and legumes.

The Gluten and Dairy Removal Comparison


Feature	Benefits of Removal	Risks of Removal	Who benefits most?
Digestive Health	Reduced bloating, gas, pain; improved regularity; gut healing	Temporary digestive upset during transition; constipation if fiber is not replaced	Those with celiac disease, lactose intolerance, or NCGS
Inflammation	Reduced systemic inflammation; potential relief from joint pain	None if managed properly, but benefits may not be noticeable for all
Energy & Mood	Increased energy levels; reduced fatigue and 'brain fog'; improved mood,	None, but may not see significant improvement if diet was already healthy	Those with existing fatigue or brain fog symptoms related to sensitivities
Nutrient Intake	Can increase diversity with whole food focus	Potential deficiencies in calcium, Vitamin D, B vitamins, iron, and fiber if not planned properly	Everyone, as long as care is taken to replace nutrients
Weight Management	May lead to weight loss by eliminating processed foods	Potential weight gain if relying on high-calorie GF/DF alternatives	Those aiming for a cleaner diet, not just weight loss

The Role of Gut Health and Microbiome Changes

Going gluten-free and dairy-free can significantly alter the composition of your gut microbiota. For some, this can be beneficial, particularly in cases of inflammatory conditions. However, studies on healthy individuals have shown that a gluten-free diet can sometimes decrease the population of beneficial bacteria like Bifidobacterium and Lactobacillus, while increasing potentially unhealthy ones. This underscores the importance of not just eliminating foods but replacing them with a wide variety of fibrous fruits, vegetables, and whole grains like quinoa, buckwheat, and millet to nourish a healthy gut. The diet's impact on gut health is complex and depends heavily on what is eaten in place of the removed items.

Conclusion: Is it Right for You?

What happens to your body when you cut out gluten and dairy depends entirely on your unique physiology, existing health conditions, and how you approach the transition. For those with diagnosed conditions like celiac disease or lactose intolerance, it is a necessary and often life-changing shift that can alleviate symptoms and promote healing. For others without a specific medical diagnosis, the results can be more varied. While some experience significant improvements in digestion, energy, and inflammation, others may notice little change or, if not careful, experience nutritional setbacks. A successful outcome relies on a well-planned diet rich in whole foods, not simply replacing one set of processed items with another. It's best to consult a healthcare professional or registered dietitian before making drastic dietary changes to ensure you maintain a balanced and nutrient-rich eating plan.

Consult a professional for personalized advice: Johns Hopkins Medicine on Gluten-Free Diet

Frequently Asked Questions

Yes, it can, but it's not guaranteed. Any weight loss is often a result of eliminating processed foods that contain gluten and dairy, and focusing instead on lower-calorie, nutrient-dense whole foods. Relying on high-calorie, processed gluten-free and dairy-free substitutes can actually lead to weight gain.

People with diagnosed celiac disease or lactose intolerance must follow these dietary restrictions. Additionally, individuals experiencing unexplained digestive issues, chronic fatigue, or skin problems may benefit, especially if testing for sensitivities or allergies is considered. However, the diet isn't universally necessary or beneficial.

Challenges include avoiding hidden gluten and dairy in processed foods, maintaining adequate intake of nutrients like calcium and fiber, and navigating social situations like eating out. Careful planning and label reading are essential for success.

Some people report experiencing temporary symptoms like headaches, dizziness, or fatigue when first eliminating gluten and dairy. These tend to resolve as the body adjusts, usually within a few weeks.

Excellent non-dairy calcium sources include leafy greens like kale and spinach, fortified plant-based milk alternatives (almond, soy, oat), tofu, and sardines. It's also vital to ensure adequate vitamin D intake for proper calcium absorption.

Results vary depending on the individual and the severity of their initial symptoms. Some people notice improvements in digestive issues within a few weeks, while significant healing, particularly for celiac disease, can take months or even years.

Yes, studies have shown that a gluten-free diet can alter the balance of bacteria in the gut. While it can be helpful for inflammatory conditions, it can also decrease populations of some beneficial bacteria. A diverse intake of fiber-rich, naturally gluten-free foods is key to supporting a healthy microbiome.