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7 Causes of Candida Overgrowth & How to Address Them

Written by Dr. Michael Ruscio, DC on April 25, 2025

Written by Dr. Michael Ruscio, DC on April 25, 2025 — Reviewed by Kellie Blake

• What Is Candida?|
• Symptoms of a Candida Overgrowth in the Gut|
• 7 Possible Causes|
• 5 Steps to Healing|

In the clinic, we often meet patients who struggle with symptoms like gas, bloating, diarrhea, skin rashes, joint pain, and brain fog. Many of them have been diagnosed with a Candida overgrowth in the gut, based on stool or urine testing. They’ve already been told to follow a strict diet and take various herbal supplements to kill the Candida. 

Though I also use diet and supplements when treating a Candida overgrowth, my goal is different. Rather than trying to eradicate Candida, I want to restore balance in the gastrointestinal (GI) tract so this yeast can peacefully coexist with other gut microbes—because Candida isn’t always bad.

In fact, Candida is a normal member of the GI tract and likely plays a helpful role—as long as other gut microbes keep it in check. But when our lifestyle or diet gets out of balance, so can our helpful gut microbes, and this is when Candida may start to overgrow and cause symptoms. 

Let’s break down what Candida is, the main factors that might cause an overgrowth in the gut, and—most importantly—how to get things back on track. 

What Is Candida?

Candida is a yeast—a type of fungus—that can live in the digestive tract, on the skin (think armpits), and in the reproductive system, and it sometimes causes infections.

The gastrointestinal tract is home to many microbes. Bacteria make up the bulk of them, but we also have around 200 types of fungi living in our guts 1. Many kinds of Candida live there, but Candida albicans seems to be the most common yeast species in a healthy gut 2. 

You read that right: Candida is supposed to be in the GI tract—about 83% of healthy people have it 3. It’s also found normally on the skin 4 and in the vagina 5. I know this may come as a surprise based on common fears of Candida, but research suggests it’s a regular member of our gut flora and not necessarily something we need to fear.  

If the gut bacteria are out of balance—a state called dysbiosis—and there aren’t enough beneficial microbes to keep Candida under control, it can start to overgrow. But it’s important to keep things in perspective: A Candida overgrowth is usually not the root cause of gut issues 6. It’s more accurate to think of it as a side effect of overall microbial dysbiosis. 

Candidiasis vs. Candida Overgrowth

I’ll clarify that Candida overgrowth is not the same as invasive candidiasis. Invasive candidiasis is a severe infection people often get in the hospital, and it can lead to life-threatening problems if not treated quickly 7.  

When I talk about a Candida overgrowth in the gut, I’m referring to high levels of this yeast in the small and large intestines. However, Candida can also overgrow in areas like the esophagus, genitals (as a yeast infection), and mouth (as oral thrush). 

Now, I’ll talk about how to know if you have a Candida overgrowth in your gut. 

Signs & Symptoms of a Candida Overgrowth in the Gut

Diagnosing a Candida fungal infection in the gut can be tricky because there aren’t any validated testing options for detecting it 8. Directly sampling the gut is probably the most accurate option, but it’s invasive and impractical. 

That may be why many healthcare providers turn to stool, urine, or food sensitivity tests. However, I want to emphasize that these tests don’t actually tell you anything useful about how much Candida is in your gut 8. 

Since Candida is a normal part of the gut microbiome, seeing it on test results can scare people for no good reason. Plus, we don’t even know what a “normal” amount is because each person’s microbiome is different. That’s why paying attention to symptoms is often a better way to tell if Candida is out of balance. In fact, research shows that these symptoms can do a pretty good job of indicating microbial overgrowths:

• Oral thrush
• Digestive problems (pain, gas, bloating, nausea, diarrhea) 9
• Worsened symptoms of irritable bowel syndrome and inflammatory bowel disease 10 11
• Anxiety 12
• Depression 13
• Chronic fatigue 14
• Brain fog 15 16
• Vaginal yeast infections 17
• Discolored, brittle nails 18
• Food intolerances
• Carb cravings

Gut issues are usually complicated, so a Candida overgrowth probably isn’t the only thing causing your symptoms. It’s more likely that your whole gut ecosystem is out of whack—and that’s what really needs fixing. 

To show you how I help restore balance in the gut, let’s examine what typically causes a Candida overgrowth in the gut. 

7 Possible Causes of a Candida Overgrowth in the Gut

Some Candida most likely helps keep the gut healthy, but it only works well when there’s a proper balance. If things start to become one-sided, a host of problems can arise. 

But why does the gut ecosystem get out of balance in the first place? Most of us can point to seven main possible reasons:

1. Acid-lowering medications

Normally, stomach acid helps kill the harmful bacteria and fungi on our food so they don’t spread through the rest of the GI tract. But acid-lowering medications make the stomach less acidic, which can create the perfect environment for bacteria and fungi to grow and spread further down the digestive tract 9. 

2. Chronic stress

Chronic stress weakens the immune system, which is like the gut’s police force. One of the immune system’s jobs is to keep gut microbes in balance. But when chronic stress wears down the immune system, it can’t do that job as well, making it easier for things like Candida to overgrow 19.

3. Antibiotics

Antibiotics kill bacteria, but many gut bacteria are important for keeping fungus levels in check. When we lose beneficial bacteria during antibiotic treatment, Candida can start to grow out of control 20.

4. Lack of physical activity

People who exercise regularly tend to have more gut bacterial diversity and a healthier gut microbiome than people who aren’t active. A diverse gut microbiome with plenty of beneficial bacteria helps keep Candida levels where they should be 21.

5. Alcohol

Drinking alcohol, especially large amounts, can cause inflammation in the gut. This can throw off the balance of gut microbes, creating an environment where Candida can grow out of control 22. 

6. Diets high in fat, sugar, and processed foods

Eating a typical Western diet—low in nutrients and high in fat, sugar, and ultra-processed foods—may increase the risk of leaky gut. This can encourage an unhealthy balance of gut microbes and allow harmful ones to overgrow 19.

7. Smoking

Tobacco smoke may disrupt the balance of gut microbes, creating dysbiosis. This imbalance may pave the way for fungal overgrowths 23.

I want to emphasize that all of the above risk factors—not just a Candida overgrowth—can contribute to an imbalance in the gut. If you’ve been diagnosed with a Candida overgrowth in the gut, it’s easy to get caught up in fear and desperation, trying anything to kill the Candida. But focusing only on killing it probably won’t lead to complete healing. 

The key point here is that, instead of blaming Candida alone, we should focus on improving overall gut health to restore balance in the gut’s microbial ecosystem. 

The great news is that many natural options can help get gut health back on track. If you’ve been struggling with the symptoms of a Candida overgrowth in your gut, my book, Healthy Gut, Healthy You, provides a step-by-step guide for healing your gut and restoring vibrant health. 

But you don’t have to wait—there are simple therapeutic strategies you can start using today to feel better. Let’s dive into them.

Healing a Candida Overgrowth in the Gut: A 5-Step Process

Instead of focusing only on Candida, our goal is to address the root causes that affect the environment along the GI tract. Since an unhealthy diet, lack of exercise, and unmanaged stress have a huge impact on gut health, I like to start by tackling these first. 

Step 1: Candida Diet

In my experience at the clinic, diet is by far the most important factor in improving gut health (and overall health). 

When it comes to a Candida overgrowth in the gut, there’s often confusion about which diet is best. Most of the clients I see with Candida symptoms have been advised to follow a very restrictive diet that cuts out all sugars and starches. But in most cases, this isn’t necessary. 

Based on a study 24 showing that people with Candida overgrowth did better when they ate a whole-foods diet—including moderate amounts of fruit, grains, and potatoes—our clinic developed a simpler, less restrictive Candida Diet. It focuses on reducing, but not completely cutting out, carbohydrates and sugars. 

By following a nutritious whole-foods diet that allows some high-quality carbs for energy, the gut ecosystem may begin to return to balance. Once that happens, the diet can expand to include a broader range of healthy foods. 

Other diets besides our Candida diet can work, too. Any diet that eliminates processed foods and added sugar should help the gut achieve better microbial balance, which is our goal when dealing with a Candida overgrowth in the gut. 

For example, these diets are also good at helping to reduce Candida in the gut: 

• The Paleo Diet
• The Low FODMAP Diet

Step 2: Lifestyle Tips

While my clients improve their diet, I coach them on ways to move their bodies every day. Exercise can increase gut microbial diversity, and more healthy gut bacteria do a better job of controlling Candida 25. 

Clients who are new to exercise can start by walking as much and as often as possible. Once we get that foundation in place, they can experiment with other types of cardiovascular training and resistance training. 

Exercise can also help us reduce stress 26, and since unmanaged stress weakens the immune system and harms gut health, staying active is beneficial for both 27. 

Because stress is a natural part of daily life, I recommend that my clients add a daily stress management practice alongside exercise. Simple activities like a short daily meditation 23, yoga 28, or spending time in nature 29 can help restore a balanced stress response and improve gut-related symptoms. 

Once we’ve addressed their diet and lifestyle, if a client still has symptoms of a Candida overgrowth in the gut, it’s time to try probiotics.

Step 3: Probiotics

Probiotics have a wide range of ways to restore balance in the gut. They’re antibacterial, antifungal, and anti-inflammatory, and they can help heal a leaky gut and support the gut’s immune system. These properties make probiotics an excellent option for relieving Candida overgrowth symptoms. 

Although we’re still waiting for research to show that probiotics can treat a Candida overgrowth in the gut, other studies support using probiotics for Candida overgrowths in the mouth 30 and vagina 31. They may even work as well as common antifungal medications like fluconazole or nystatin 31 32.

In the clinic, we use a triple-therapy protocol, meaning we recommend three main categories of probiotics together. This means taking a blend of Lactobacillus and Bifidobacterium strains, Saccharomyces boulardii (a beneficial yeast), and soil-based probiotics (Bacillus species) for 2–3 months.

If our clients don’t find that a healthy diet, lifestyle, and probiotics are enough to get rid of their Candida overgrowth symptoms, I suggest they consider trying an elemental diet.

Step 4: Elemental Diet

If Candida overgrowth symptoms linger after steps 1–3, inflammation in the GI tract is probably why. An elemental diet can help to calm that inflammation and allow the intestines to heal.

An elemental diet is a hypoallergenic, anti-bacterial, and anti-inflammatory meal replacement that can help improve a variety of digestive and other issues 33 34 35 36. It provides essential nutrition while giving the small intestine a break from digestion and by limiting the activity of harmful microbes like Candida 37. 

In a study of children with Crohn’s disease, a weeklong elemental diet appeared to reduce their Candida levels, even if they ate normal meals some of the time 38. We’ve also seen a reduction in Candida overgrowth symptoms when our clients follow an elemental diet, either full-time or part-time.

One note of caution if you have a Candida infection of the mouth: The sugar in an elemental formula may make oral thrush worse, so I wouldn’t recommend using it. 

The final step to consider when treating a Candida overgrowth in the gut involves antimicrobials.

Step 5: Antimicrobials

Antimicrobials include a variety of plant-based extracts and medications—like antibiotics and antifungals—that are designed to kill harmful bacteria and other microbes 39. 

You might be wondering, Why not just start with antimicrobials to get rid of Candida? From our experience in the clinic, jumping straight to antimicrobials often sets people up for failure long-term. 

Here’s why: If we skip the basics—like improving the diet and lifestyle—and go straight to attacking gut Candida with antimicrobials, we’re not addressing the root cause, which is poor gut health. Even if antimicrobials kill the Candida, they can also harm the beneficial microbes that help keep your gut in balance. Without those good microbes, things can spiral and leave you worse off than before.

That’s why we hold off on antimicrobials until the gut has a stronger foundation. And when the time is right, I typically recommend herbal antimicrobials over pharmaceuticals. Herbal options tend to cause fewer side effects 40, are less likely to lead to antimicrobial resistance 41 42, and are generally gentler on the gut microbiome 43. 

These herbal treatments can kill Candida in the gut and get rid of the digestive symptoms that come with it 42. 

Tackle Candida Overgrowth Naturally

Candida is a natural resident of most people’s gut microbiomes. It normally lives in harmony with other gut microbes, but an imbalanced diet and lifestyle can cause it to overgrow. 

In other words, a Candida overgrowth in the gut is usually a side effect of an unhealthy gut ecosystem.

Rather than immediately targeting Candida with antimicrobials, I find clients benefit the most from building a healthy foundation for the gut first.

If you go through this process and still feel unwell, we’d love to help you on your journey. Check out my book Healthy Gut, Healthy You for my complete Great-in-8 gut healing protocol, or contact us at the Ruscio Institute for Functional Health to schedule an appointment.

The Ruscio Institute has developed a range of high-quality formulations to help our clients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you. The information on DrRuscio.com is for educational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.