Struggling with food sensitivities? Your hormones may be playing a role

The link between food sensitivities and our hormones is clear but not often discussed. How may food intolerances contribute to hormone issues?

Are you struggling with confusing and uncomfortable symptoms? It’s possible that a specific food or food category is at the root of your symptoms.

In this article, guest author Dr. Pooja Mahtani answers the following questions:

  • What is the difference between a food intolerance, food allergy, and food sensitivity?
  • What are the symptoms of food intolerance, allergies, and sensitivities?
  • How can you find the source of a food reaction and what steps can you take to improve symptoms?
  • Is there a connection between food sensitivities and our hormones?
  • How do stress and cortisol impact food sensitivities?
  • Does our thyroid impact how we react to food?
  • Do hormonal imbalances like PCOS increase risk of having a food sensitivity, intolerance, or allergy?

What are the different types of food reactions?

Before I dive into this topic, let’s define the various food reactions. The three most common reactions include food intolerances, food allergies, and food sensitivities (because yes, they are all different!):


An intolerance occurs when your digestive system is unable to breakdown certain foods. The most common reason for an intolerance is enzyme deficiency. A great example of this is lactose intolerance. Lactose is a sugar found in milk products such as milk, ice cream, and cheese. The enzyme responsible for breaking down lactose is called lactase.  When individuals have low levels of lactase, undigested lactose makes its way into the colon and our gut bacteria end up breaking down the lactose instead. As our gut bacteria break down lactose, fluid is drawn into colon. This ultimately causes gastrointestinal symptoms such as gas, abdominal pain, and diarrhea. Lactose intolerance can occur at any age, and it’s believed that genetics may play a role (1).


On the other hand, a food allergy involves the immune system. For example, if you have a peanut allergy, your immune system has identified peanuts as a “foreign invader”. It will mount a response by producing antibodies called Immunoglobulin E (IgE). These IgE antibodies will go on to elicit an allergic reaction which can take place within minutes to hours of ingesting the allergen. Unlike food intolerances, food allergies can range from mild to life-threatening anaphylaxis. Common symptoms include wheezing, hives, itchiness, skin swelling, vomiting, and diarrhea (1).


A food sensitivity is similar to a food allergy in that the immune system is involved. However, instead of triggering an IgE-mediated allergic reaction, a sensitivity is caused by other antibodies in the immune system known as Immunoglobulin G (IgG) and Immunoglobulin A (IgA). These IgG and IgA antibodies can travel throughout the body and generate widespread symptoms. Unlike IgE-mediated reactions, food sensitivities may be delayed in nature with reactions occurring hours to several days later. While these symptoms may not be life-threatening as an IgE-mediated allergic reaction, they can be quite diffuse and intrusive. Examples of food sensitivity reactions include joint pain, headaches, fatigue, rashes, dizziness, and brain fog (2). One of the most common food sensitivities today is gluten sensitivity. It should be noted that gluten sensitivity is different from celiac disease, which is a known autoimmune condition mediated by gluten consumption (3).

A general approach to food sensitivities

If you have a history of food sensitivities, it’s possible you have already tried a few of these initial steps.

One of the first steps in addressing a food sensitivity is eliminating the food or foods that are causing symptoms for a period of 3-6 months while addressing the other underlying factors.

The next step is to ensure you have sufficient hydrochloric acid and digestive enzymes to break down the proteins, fats, and carbohydrates in your diet. In addition, ensuring you have an intact intestinal lining and a diverse microbiome is critical for maintaining tolerance to various foods. For example, supplementing with L-glutamine, Vitamin A, Vitamin D, and fiber is a good starting point to help re-establish a strong intestinal barrier and healthy microbiome. I always recommend my clients run a microbiome stool panel such as the GI MAP by Diagnostic Solutions to understand the state of their microbiome.

Another aspect to managing food sensitivities is ensuring you have optimal liver detoxification function as well as antioxidant support.

If these initial steps do not eradicate your food sensitivities, then it’s time to consider hormones as a contributing factor. Cortisol, thyroid, estrogen, and progesterone all play a critical role in maintaining intestinal barrier function. Let’s take a look at exactly how these hormones contribute to the development of food sensitivities.

Stress is a major trigger for food sensitivities

Chronic stress is one of the most significant risk factors for developing food sensitivities. This is something that I see in my practice all the time. But what are the steps to stress leading to food sensitivities?

Cortisol, our body’s master stress hormone, is responsible for decreasing Secretory Immunoglobulin A (sIgA), an immune antibody found all throughout our mucosal barriers including the eyes, mouth, sinuses, throat, GI tract, respiratory system, vaginal tract, and urogenital tract. Think of sIgA as our first line of immune defense. Under chronic stress, elevated cortisol can significantly reduce sIgA production. Without this first line of defense, cortisol can begin to disrupt the integrity of our intestinal lining and cause a phenomenon known as intestinal permeability, or more commonly known as “leaky gut syndrome” (4).

A leaky gut then allows larger food proteins to enter the bloodstream. Once these larger food proteins are in the bloodstream, our immune system can mount an inflammatory response against these “foreign invaders”. In turn, this inflammatory response can manifest as various symptoms such as joint pain, headache, eczema, brain fog, and mood disturbances such as anxiety and irritability. These symptoms are ultimately classified as food sensitivity reactions.

Unfortunately, our bodies cannot distinguish between the various kinds of stressors (emotional, physiological, or physical). These different types of stressors can all trigger a release of cortisol. One of the most stressful events our bodies routinely experience is dysglycemia, or blood sugar imbalance. A common dysglycemia pattern is hypoglycemia, or low blood sugar.

Common symptoms of hypoglycemia include irritability (a.k.a hanger), hunger, anxiety, shakiness and fatigue. Every time our bodies enter a hypoglycemic state, our adrenals release cortisol to help stabilize our blood sugar levels. This gives us a temporary boost in blood sugar, and as a result, a temporary boost in energy as well (5,6).

Now imagine a person who always rushes in the morning, skips breakfast, and drinks coffee on their way out the door. The lack of calories in the morning and caffeine consumption begins to put pressure on the adrenals to release excess cortisol to help maintain steady blood sugar levels. Next this person eats a wrap and drinks a sweetened iced tea for lunch. This meal is high in refined carbohydrates and will likely cause their blood sugar levels to skyrocket. However, just as quickly as blood sugar rises, it will drop due to the surge in insulin that follows. After lunch, this person will likely crash in the afternoon and once again cortisol will need to come to the rescue to help stabilize blood sugar levels. Eventually, this person may reach for a quick fix like a granola bar to get a burst of energy. But again, this spike in blood sugar will quickly drop due to the subsequent surge in insulin.

This yo-yo blood sugar cycle puts constant pressure on the adrenals. Over time, this chronic stress will decrease sIgA levels along the intestinal lining, promote intestinal permeability, and likely contribute to the development of food sensitivities.

Thyroid hormones can also promote food sensitivities

Hypothyroidism secondary to Hashimoto’s disease, an autoimmune thyroid disease, is a significant cause for food sensitivities.

In a hypothyroid state, a person has inadequate levels of T4 and T3 thyroid hormone. T3 hormone is our active thyroid hormone, and it is derived from T4 thyroid hormone. It’s actually our T3 thyroid hormone that plays a significant role in maintaining the intestinal lining. The lack of adequate T3 thyroid hormone can cause immune dysregulation along the gut lining, suppression of digestive enzyme release, and ultimately give rise to intestinal permeability (7). All of these downstream effects of low T3 thyroid hormone can promote the development of food sensitivities.

In the majority of autoimmune thyroid cases, there is usually an underlying inflammatory mechanism that is down regulating the conversion of inactive T4 thyroid hormone to active T3 thyroid hormone (8). Examples of inflammatory mechanisms include chronic stress, a poor diet, gluten sensitivity, an imbalanced microbiome, a viral infection like Epstein-Barr Virus, or high levels of environmental toxin exposure like glyphosate.

In other words, if you are struggling with both hypothyroidism and food sensitivities, it is critical to re-establish optimal T3 thyroid hormone levels first. Once your thyroid hormones are optimized, it becomes much easier to address the food sensitivities. In several cases, I have seen that addressing the thyroid eliminates the food sensitivities all together!

A clarifying point: Gluten sensitivity is both a food sensitivity as well as a major trigger for Hashimoto’s disease. If you are struggling with Hashimoto’s as well as significant food sensitivities, it will very likely be a challenge to reintroduce gluten back into your diet. While other food sensitivities can be addressed and healed over time, you will likely need to avoid gluten for the long-term to keep your Hashimoto’s well managed.

Sex hormones also play a role (specifically in histamine driven reactions)

It’s possible the food sensitivity you may be struggling with is actually a histamine intolerance. So, what exactly is histamine intolerance?

Let’s start with histamine. Histamine is a chemical compound stored in our mast cells and other immune cells. Histamine is likely best known for its role in allergic reactions. When histamine is released from mast cells, it can trigger an allergic response and cause symptoms such as vasodilation, swelling, allergic rhinitis, itching, hives, asthma, and in severe cases, anaphylaxis. In addition to eliciting an allergic reaction, histamine also has several other functions in the body, namely modulating brain health, immunity, and stomach acid secretion (9).

We produce histamine naturally in our bodies. We also consume histamine through foods such as aged and fermented foods, alcohol, eggplant, spinach, canned fish, and tomatoes (9).

The body metabolizes histamine through two enzymes, histamine N-methyltransferase (HNMT) and diamine oxidase (DAO). So, despite the name, histamine intolerance is not a true “intolerance” to histamine. Instead, histamine intolerance develops when there is more histamine in the body than can be effectively broken down by these two enzymes (9). The most common cause for histamine intolerance is gut dysbiosis, or an imbalanced microbiome (10).

While symptoms of histamine intolerance may vary, some common symptoms include asthma, nasal congestion, headaches, diarrhea, fatigue, low blood pressure, hives and/or itching, anxiety, and irregular menstrual cycles (9).

So, how is histamine intolerance connected to our sex hormones? Believe it or not, our mast cells have receptors for both estrogen and progesterone. When estrogen binds to the mast cell receptor, it causes more histamine to be released. At the same time, estrogen also has the ability to influence and often down-regulate DAO enzyme activity, one of the main enzymes responsible for breaking down histamine (11). Furthermore, the relationship between histamine and estrogen is bidirectional. By signaling the ovarian cells (yes, ovarian cells have a histamine receptor!), histamine can induce estrogen synthesis (9).

As you can imagine, this creates a vicious estrogen-histamine cycle. On the other hand, progesterone has the ability to reduce histamine levels. While DAO enzymes fluctuate throughout the menstrual cycle, they are at their peak during the luteal phase or progesterone dominant phase (12). This fluctuation is fine if your sex hormones are balanced, but if you are struggling with hormone imbalance, you may be more prone to histamine intolerance.

One of the most common hormonal imbalances women face today is estrogen dominance, the state of having too much estrogen in relation to progesterone. Interestingly, women with histamine intolerance tend to experience more headaches during peak estrogen times such as ovulation or right before menstruation. These are the same women who tend to present with estrogen dominance. Histamine can also increase contraction of smooth muscle cells and cause more menstrual cramping. This occurs more frequently in women with estrogen dominance (9). My favorite test to help identify estrogen dominance is the DUTCH Complete by Precision Analytical.

While working to address histamine intolerance, many women find relief by adopting a low-histamine diet. By eliminating foods that are high in histamine, you can reduce the amount of histamine in the bloodstream that your body has to eliminate. This is an effective short-term approach while working to identify the root cause of your histamine intolerance.

A special note about PCOS

The most common hormonal imbalance in women giving rise to food sensitivities is polycystic ovarian syndrome (PCOS). In women with insulin-resistant PCOS, the pattern of dysglycemia will once again trigger intestinal permeability and lead to the development of food sensitivities. In this case, insulin resistance will promote hyperglycemia, or too much blood sugar in the bloodstream.

Remember insulin’s job is to escort glucose into the cell. When the cell becomes resistant to insulin, glucose can no longer enter the cell. Instead, we are left with excess sugar in our blood stream for a period of time until the body can redirect the glucose to other areas.

For example, some of the glucose is taken up by the liver and converted to glycogen, a storage form of glucose that can be used later when energy needs are critical. Glucose is also taken up by the liver and converted into triglycerides, a storage form of fat. The remaining glucose is taken up by adipocytes, our fat cells, and stored as fat (13).

While the body is figuring out where to redirect this glucose after a meal, this temporary hyperglycemic state can trigger intestinal permeability (14). In fact, studies show that the higher the hemoglobin A1c, a measure of blood sugar over a 3-month period, the greater the degree of intestinal permeability (15).

When it’s time to consult with a practitioner specializing in a functional medicine approach

If you do not see improvements in your food sensitivities after trying an elimination diet, I encourage you to work with a practitioner that specializes in a functional medicine approach.

You may require in-depth functional testing that evaluates your adrenal, thyroid, and sex hormones as well as your microbiome status.

With this testing data, your practitioner can then help you decode your food sensitivity symptoms from a whole body systems perspective, and offer a comprehensive diet, supplement, and lifestyle program that helps you finally put your food sensitivity symptoms into remission, and allows you to resume a diet that is abundant in a variety of foods.


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Dr. Pooja Mahtani

MS, CNS, LDN, PharmD

Dr. Pooja Mahtani is the founder of Pooja Mahtani Wellness, a virtual functional nutrition practice that specializes in gut, immune, and hormonal health. Dr. Mahtani is a Board Certified Nutrition Specialist® and Licensed Dietitian Nutritionist. She also holds a Doctorate in Pharmacy and Master’s in Human Nutrition along with extensive training in functional nutrition from the Institute for Functional Medicine.