Why Does Metformin Cause Diarrhea? Here’s What Happens in Your Gut

Metformin is one of the most commonly prescribed medications for managing type 2 diabetes, helping millions of patients control their blood sugar effectively. However, many people experience metformin-induced diarrhea, bloating, and stomach upset, which can make daily life uncomfortable.

Metformin is a widely prescribed oral medication for managing type 2 diabetes. It helps lower blood sugar by improving the body’s insulin sensitivity and reducing glucose production in the liver.

Often recommended when diet and exercise alone aren’t enough, metformin is also used to support fertility in individuals with polycystic ovary syndrome (PCOS) by regulating insulin and promoting ovulation.

Understanding why metformin causes diarrhea and learning simple strategies to manage these side effects can help patients continue their treatment safely.

Metformin is available in multiple forms, including standard tablets, extended-release tablets, suspensions, and solutions. To reduce gastrointestinal discomfort, it’s usually taken with meals. Pharmacist Ethan Melillo also notes that patients should ideally start on the lowest dose, typically 500 milligrams, and take it with food to minimize stomach issues. Whenever possible, switching to an extended-release formulation may further reduce gastrointestinal side effects.

Pharmacist Ethan Melillo, known on social media as @millennialrx, breaks down exactly why metformin makes you go to the bathroom more often. He explains that the medication changes how your gut uses sugar, increases gas and acid production, and even speeds up digestion.

Ethan explains:

Melillo says that Metformin can affect the way your body processes bile salts, which are made in the liver to help digest fats. Normally, these bile salts are recycled by the body, but metformin can interfere with that process.

When more bile salts reach the lower intestines, they attract extra water, which can make your stool looser and sometimes cause mild diarrhea.

He further adds that metformin may increase serotonin levels in the gut, which speeds up intestinal movement. This faster transit time means the body has less opportunity to absorb water from stool—one reason patients experience loose or runny stools.

Some patients may be more prone to gastrointestinal side effects because of genetic differences in intestinal drug transporters. Variants in the organic cation transporter 1 (OCT1) have been associated with higher intestinal concentrations of metformin and increased risk of GI intolerance, including diarrhea. ²

• Beyond blood sugar control: Metformin also influences gut health and microbial balance—a lesser-known but important effect that may contribute to both its benefits and side effects.

• Changes in gut bacteria: Studies show that metformin can alter the composition of gut microbiota, increasing beneficial bacteria.

• Impact on insulin sensitivity: These microbial shifts may help enhance insulin sensitivity and improve glucose regulation in people with type 2 diabetes.

• Possible link to side effects: Some gastrointestinal effects, such as bloating or diarrhea, may result from how metformin interacts with gut bacteria. ¹

Ethan explains "But metformin can change the balance of these bacteria, and with this off-balance of bacteria in your gut, it can either make your gut work faster or create more gas."

Recent research (2024–2025) has reinforced that metformin consistently alters the gut microbiome, often increasing mucin-degrading and short-chain fatty acid–producing genera such as Akkermansia and Roseburia, changes that may both mediate beneficial metabolic effects and contribute to gastrointestinal symptoms in some patients. ³ ⁴

Metformin also appears to reduce bile acid reabsorption in the small intestine, a mechanism that can produce osmotic diarrhea in susceptible individuals by increasing bile acids in the colon and drawing water into the stool. ²

Altogether, these combined effects—on sugar metabolism, bile salt recycling, gut bacteria, and intestinal motility—explain why many patients initially experience digestive discomfort when starting metformin therapy. Gradually increasing the dose and using extended-release versions can often help the body adapt and minimize these issues.

When to Worry: Red Flags and When to Seek Medical Advice

Most metformin-related diarrhea is mild and improves with dose adjustments or switching to an extended-release formulation. However, seek medical advice if you experience any of the following: persistent diarrhea lasting more than a week despite dose changes; signs of dehydration (dizziness, very dark urine, low urine output); severe abdominal pain; blood in stool; unexplained weight loss; or symptoms of lactic acidosis such as profound weakness, muscle pain, breathing difficulty, or confusion. ⁵

If diarrhea is chronic or severe, clinicians may evaluate for bile acid malabsorption or other causes and consider stopping metformin temporarily while investigating. ² ⁵

Takeaway

Metformin remains a cornerstone therapy for type 2 diabetes. Understanding how it affects digestion can help patients manage side effects and continue benefiting from its proven glucose-lowering power.

Reference:

1. Nakajima, H., M. K. Hasegawa, H. S. Kato, Y. S. Takahashi, K. S. Tanaka, and T. K. Sato. "The Effects of Metformin on the Gut Microbiota of Patients." Frontiers in Microbiology 11 (2020): 580287. https://pmc.ncbi.nlm.nih.gov/articles/PMC7555986/

2. Szymczak-Pajor, Iwona, and Agnieszka Śliwińska. "Metformin-Associated Gastrointestinal Adverse Events Are Linked to Bile Acid Malabsorption and Transporter Variations." Pharmaceutics 17, no. 7 (2024): 898. https://www.mdpi.com/1424-8247/17/7/898.

3. Rosell-Díaz, M., et al. "Metformin-induced changes in the gut microbiome and their clinical implications." Endocrine Reviews (2024). https://pubmed.ncbi.nlm.nih.gov/38871078/.

4. Wang, Y., et al. "Understanding the action mechanisms of metformin in modulation of the gut microbiota." Frontiers in Microbiology (2024). https://www.frontiersin.org/articles/10.3389/fmicb.2024.1396031/full.

5. Chaudhary, M., et al. "Metformin-Induced Chronic Diarrhea Misdiagnosed as Other Conditions: Clinical Features and Management." Case Reports in Gastroenterology (2024). https://pmc.ncbi.nlm.nih.gov/articles/PMC11037500/.

(Rh/Eth/ARC/MSM)