Protein is fundamental to our overall health, but when it causes discomfort, it’s easy to question whether it’s right for you. In most cases, it isn’t protein that’s the issue, but how and when it’s taken. Making simple changes can often make a big difference.
To understand what’s really going on, we spoke to consultant dietitian Sophie Medlin, a leading specialist in gut health and digestion. Drawing on her clinical experience, she helps unpack protein digestion and absorption, why tolerance varies from person to person, and what often sits behind digestive discomfort.
What Happens to Protein After You Eat It?
Protein digestion is more complex than many people realise. “Unlike fats and carbohydrates,” Sophie explains, “protein can’t be absorbed whole. Instead, it is broken down into its smallest usable units, known as amino acids.”
This process begins in the stomach. Stomach acid plays a crucial role in unfolding complex protein structures, allowing an enzyme called pepsin to start cutting them into smaller fragments called peptides.
Once these partially digested proteins move into the small intestine, the pancreas releases additional digestive enzymes. These enzymes break peptides down further into single amino acids and very small chains (di-peptides and tri-peptides), which can then be absorbed across the gut wall and into the bloodstream.
After absorption, amino acids are used throughout the body to:
Support muscle repair and maintenance
Build enzymes and hormones
Support immune function
Maintain skin, hair, and connective tissue
Digestions vs Absorption: Does the Difference Matter?
A common source of confusion in gut health conversations is the difference between digestion and absorption.
“In general, public literacy around digestion and gut health is limited,” Sophie explains, “which leaves people confused and vulnerable to misinformation.”
Sophie clarifies the difference simply:
Digestion is the process of breaking protein down into amino acids
Absorption is the process of pulling those amino acids across the gut lining and into the bloodstream
Many people assume that if protein causes discomfort, it isn’t being absorbed properly. However, most people have a healthy gut lining that protein can cross to reach the bloodstream. Digestive discomfort is therefore likely to have another cause.
Why Gut Function Shapes How Well Protein is Tolerated
How well the gut breaks down and absorbs protein can vary from person to person. Individual variability in both digestion and absorption can affect how well you feel you tolerate protein.
How can digestive enzymes affect protein digestion?
Digestive enzyme levels can affect how efficiently protein is processed.
“Some people naturally produce fewer digestive enzymes due to genetics, medical conditions, or medications such as PPIs, which reduce stomach acid production,” Sophie tells us.
It is normal for levels of digestive enzymes to vary. This is one reason protein digestion may differ between individuals.
How does the lining of the gut affect absorption of protein?
Inside the small intestine are millions of tiny finger-like structures called villi, covered in even smaller microvilli. Together, they increase the surface area of the gut, trapping nutrients and allowing the amino acids to enter the bloodstream.
A healthy gut lining:
Maximises the volume of nutrients entering the bloodstream
Contains specialised transporters to move amino acids to the bloodstream
Acts as a selective barrier to keep harmful substances out
Sophie is keen to clarify a common misconception here. Despite what alternative practitioners on social media might suggest, most people do not have a damaged or “leaky” gut lining.
“In reality, impaired gut lining function mainly affects people with conditions like inflammatory bowel disease or unmanaged coeliac disease,” she says. “The vast majority of people have a healthy gut lining and other reasons for digestive symptoms.”
Why Does Protein Cause Bloating or Discomfort for Some People?
Experiencing bloating, gas, or discomfort after taking protein doesn’t automatically mean protein is the problem.
In Sophie’s clinical experience, the most common culprit is lactose, a carbohydrate found in dairy-based proteins like whey.
“Lactose intolerance is about the lack of the enzyme lactase, not a problem with protein itself,” she confirms.
Many adults produce less lactase as they get older. Some are mildly lactose intolerant and only notice symptoms with larger amounts of dairy.
Other factors can also play a role, including:
Drinking protein very quickly
Consuming a lot of dairy at once
Combining protein shakes with other dairy-heavy meals
Temporary lactose intolerance after illness or food poisoning
Importantly, these symptoms are uncomfortable but not harmful, and they don’t mean protein isn’t being absorbed or used.
Can Changing Your Protein Routine Improve Comfort?
One of the simplest ways to improve protein tolerance is to consider when and how it’s consumed.
Sophie notes that if you know you’re sensitive to lactose, it’s worth taking a protein shake at a different time to a main meal, especially if the meal also contains dairy. The extra protein could push someone past their personal threshold for lactose tolerance, causing some discomfort.
For many people, protein is better tolerated:
Between meals, rather than alongside them
In smaller doses, spread throughout the day
As part of a consistent routine, not occasional large intakes
Despite common myths, there’s no hard limit on how much protein the body can absorb at once. Sophie confirms that, “we only need 20-40 grams of high-quality protein, such as whey protein, at a time, to maximally stimulate muscle growth and repair.” Excess protein will still be absorbed, but used for other functions.
Does Gut Health Influence Whether Protein Feels Like It’s Working?
Your enjoyment of protein might be affected by lactose, but it doesn’t usually determine whether your body can use the protein or not.
“Unless you have a severe digestive problem such as inflammatory bowel disease or unmanaged coeliac disease, your body will be absorbing and utilising all the protein you are consuming,” Sophie reassures.
Protein works best when paired with:
Weight-bearing or resistance exercise
Adequate recovery
Consistently taking protein
If you notice digestive problems like bloating, gas, loose stools or constipation, Sophie recommends trying a lactase enzyme tablet. Lactase breaks down lactose, making it easier to digest and preventing digestive symptoms.
The benefits of protein often show up gradually, rather than as an immediate sensation.
To find out more about why it can feel like protein isn’t working, read our article: Why Don’t Some People Feel the Benefits of Protein Straight Away – and How Can That Be Fixed?
Making Sense of Protein, Gut Health, and Comfort
When protein feels uncomfortable or ineffective, it’s easy to assume something is wrong with your gut. But the explanation is usually far more ordinary. Digestion varies, tolerance thresholds differ, and benefits often build quietly over time rather than showing up as instant results.
By understanding protein utilisation and how gut health can influence it, it becomes easier to focus on changing how and when you use protein so that you feel more confident about including it in your diet.
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