If you have ever dealt with digestive issues, chances are that at one point or another you’ve been told by a doctor to follow an elimination diet, or have experimented on your own with cutting out various foods or food groups. Elimination diets—which temporarily remove food or food groups from your diet—are considered the “gold standard” for pinpointing food intolerances and allergies among gastroenterologists and other gut health experts. Why? They’re typically non-invasive and don’t require any expensive testing, making them an easily accessible diagnostic tool.

How elimination diets work is that certain foods are initially eliminated from your diet, then gradually reintroduced to help you better identify what things might be contributing to symptoms like bloating, diarrhea, and abdominal cramping. For example, the low FODMAP diet, frequently used for those with irritable bowel syndrome (IBS), has people eliminate specific types of carbohydrates that can trigger IBS symptoms—then bring them back one by one to see what foods people can tolerate and which might exacerbate symptoms.

Each individual is unique, and sometimes it just takes some trial and error to find the right dietary approach for your body.

I’m a registered dietitian specializing in gastrointestinal (GI) health, and this “cutting foods out” approach is so common in my field that my clients are often surprised to find that I rarely recommend nixing foods from their diets. If I do, it’s usually only temporary, as part of a targeted elimination and reintroduction to pinpoint GI symptom triggers. In fact, I frequently encourage my clients to add more foods into their diet.

To be clear: Sometimes long-term dietary restrictions are a clear medical necessity, such as in the case of a food allergy, intolerance, or specific medical condition. (I would never tell someone with Celiac disease, for example, that it’s safe to keep gluten in their diet.)

That said, I am concerned at how commonly people believe that permanent restriction is necessary for gut health, especially since following these diets in the absence of medical necessity can come with some negative health consequences—and may not even provide much symptom relief.

Why dietary restrictions aren’t always the best first way to treat gastrointestinal issues, according to an RD

1. Cutting out foods doesn’t always address the full underlying problem

Digestive problems can arise for reasons other than food sensitivities and intolerances. Often, the root of GI symptoms is multifactorial¹, meaning that there are a lot of issues contributing to a person’s symptoms. I find that taking into account how we eat is just as crucial to gut health as what we eat. For example, a person with IBS might find it hugely helpful to address behavioral factors² such as meal patterns and frequency, portion sizes, and the balance of different nutrients on your plate.

Looking at other lifestyle factors such as sleep, physical activity, and psychological stress can also be illuminating. It is well-established that stress, a lack of sleep, and inactivity can impair gut motility, or our body’s ability to move food through the digestive tract properly. So elimination can only go so far if someone also isn’t sleeping well and is super stressed out.

2. Severe food restrictions reduce the diversity of your gut bacteria

The bacteria and other microorganisms living in the gut have been shown to impact everything from our digestion and immune function to our mood³. While gut microbiome research is still in its early stages, studies have repeatedly demonstrated that a diverse gut microbiome—one that is comprised of many different species of bacteria—is a healthy gut microbiome⁴. In fact, many GI conditions, such as inflammatory bowel disease (IBD)⁵ and IBS⁶, are associated with low diversity of gut microbes.

Eating a wide array of minimally processed plant foods—like fruits, vegetables, beans, grains, nuts, and seeds—is one of the best ways to support a diverse and healthy gut microbiome.⁷ Heavily restricting the variety of foods in your diet seems to have the opposite effect, and can actually harm your gut microbiome over time. Research published in the journal Nutrients in July 2019 found that following a low-FODMAP diet can reduce gut bacteria diversity in as little as two to three weeks⁸. Another study published in the journal Clinical Gastroenterology and Hepatology in March 2022 found that people with IBS who followed restrictive diets had a lower abundance of certain “good” bacteria strains in their gut⁹, like Lactobacillus (which is anti-inflammatory and protects your gut barrier¹⁰), compared to those with IBS who did not follow a restrictive diet.

Research published in the journal Nutrients in July 2019 found that following a low-FODMAP diet can reduce gut bacteria diversity in as little as two to three weeks.

Cutting out these foods or food groups temporarily likely won’t have a long-term negative impact on your gut. (When you start adding back foods, your gut bacteria will be able to flourish.) But I’ve found that over-restriction can lead to a vicious cycle over time: the more foods you eliminate, the less diverse your gut microbiome becomes and the more likely you are to experience unpleasant GI symptoms.

3. Eliminating food groups can put you at risk of nutrient deficiencies

Beyond benefiting your gut microbiome, each variety of whole, minimally processed food contains a different nutrient profile. If you’ve cut out multiple foods or food groups, you’ll have a harder time getting the key nutrients your body needs to function optimally. In fact, one of the best ways to ensure that you’re meeting your nutrient needs is to eat a diverse array of whole foods.

Your energy levels and mental clarity can take a major hit when you aren’t fueling your body properly. Plus, nutrient deficiencies can lead to more serious health consequences down the road if not addressed. For example, those on a low-FODMAP diet for a prolonged period without food reintroductions might not be getting enough fiber, antioxidants, calcium, iron, zinc, B vitamins, or vitamin D. Falling short on these key dietary components can lead to constipation, low bone mineral density, and fatigue.

4. Restrictive diets can harm your emotional health, too

Not only can overly restrictive diets pose negative consequences on your physical health, they may also take a significant toll on mental health, negatively impacting quality of life. Social events, holidays, and family celebrations are often centered around food, and when you’re following a highly restrictive diet, these food-centric gatherings become stressful. Meal planning and preparation also becomes increasingly challenging the more limited your diet is.

If you’re struggling with gut issues and over-restriction, you certainly aren’t alone. In fact, compared to the general population there is a higher prevalence of eating disorders among people with GI conditions, such as IBS and IBD. It’s understandable that regularly experiencing uncomfortable symptoms after eating can put a strain on your relationship with food, and the added stress of following a strict elimination diet often makes things worse.

Not everyone with digestive issues is an appropriate candidate for an elimination diet, which is why it’s helpful to seek guidance from a trusted professional for proper evaluation when it comes to nutrition and digestive troubles.

Not everyone with digestive issues is an appropriate candidate for an elimination diet, which is why it’s helpful to seek guidance from a trusted professional for proper evaluation when it comes to nutrition and digestive troubles. Registered dietitians specialized in digestive health and disordered eating can work with you to address your specific symptoms and concerns in the least restrictive way possible, to avoid triggering disordered eating behaviors.

How I help my patients’ gut health with minimal restriction

Again, true food allergies and certain other medical conditions can require cutting out certain foods altogether. But typically, I work on a number of different strategies with clients to help them feel better without having to give up all of their favorite foods.

For example, if you have trouble digesting certain foods, you may not necessarily need to avoid these foods forever. Our food tolerance can improve over time as our gut microbes shift and become more efficient at breaking down food components. If I had a client realize that eating beans makes them feel uncomfortably bloated and gassy, I’d have them try incorporating tiny portions into their meals each day rather than cutting them out altogether. Gradually increasing portion sizes over time might help them learn to tolerate beans—allowing them eventually to eat moderate quantities without digestive distress.

Even in the case of digestive enzyme deficiencies, enzyme replacement therapy may be available, allowing you to still enjoy foods that might otherwise cause digestive issues. For example, those with lactose intolerance can take lactase enzyme pills in order to still enjoy lactose-containing dairy products if they so choose.

For others, certain supplements and lifestyle modifications can provide significant benefits. For example, a soluble fiber supplement may help to regulate bowel motility for people with consistent constipation issues, while implementing a meal schedule can be highly effective at addressing acid reflux.

Ultimately, digestive health (and the things that affect it) is complex, and restriction shouldn’t be the only tool we have in our tool kit to address problems. Each individual is unique, and sometimes it just takes some trial and error to find the right dietary approach for your body.

—reviewed by Jennifer Logan, MD, MPH