Unplugging the Food Matrix for Nutrition and Human Health
Learn why the physical structure of food matters as much as the nutrients in it, and how the food matrix can be used to improve your health.
- Food is more than a list of nutrients; it's physical structure. This is known as the "food matrix" and can affect nutrition and your health.
- An intact or whole food matrix can slow digestion, control your appetite, and feed the "good" gut bacteria. But it's not always good!
- Smart cooking techniques and preparation methods can sometimes increase the amount of nutrients that your body absorbs.
Check the nutritional labels on the back of the food packaging. Carefully weigh the food to the nearest gram to make sure you're getting the right amount of calories and macros. Check the fat and carbs to make sure you're meeting macro targets. Or check the back to check you're getting enough vitamins and minerals.
This is what we've been told for decades. Judge a food by its nutrition label. We assume the label tells us everything, and only things that count are things that are counted on the label: the calories, the grams of protein and the milligrams of vitamins, right? The "label only" approach treats food as a sack of chemicals. It assumes that the nutritional "value" of the food is just the sum of its individual nutrients.
If this is true, 20 grams of fat from butter should have the same effect on your body as 20 grams of fat from hard cheese. And the sugar from 2 oranges should behave like the sugar from a glass of orange juice. It would be great if nutrition were this simple. However, it's not. It misses an important part of the puzzle: the "food matrix effect".
What is the Food Matrix Effect?
The food matrix is the natural physical structure of your food. It's the way all of its different parts of the food are joined together. When you eat whole food, your body isn't just digesting (and absorbing) the individual ingredients or nutrients on the label; it has to deal with the entire food matrix: a unique three-dimensional structure that contains hundreds of different things in it.
Imagine it like this. If you were to take all the things that are in an apple: the fibre, the sugar, the vitamin C, the potassium, the lignin, the cellulose, the compounds that give it its colour, and mix them in some water, you wouldn't have anything like an apple. The apple only exists because of the way that those individual parts are organised and connected. The individual nutrients in the apple are locked inside the apple's cells, lattices, or connected to other things. This is the food matrix. [1]
So, is the food matrix good or bad? The answer is neither. It can be good or bad. It depends on what food you are eating, and what nutrients you are trying to get from the food. It can work in your favour or against you. There are good things in the apple. But there are also not-so-good things. The food matrix can prevent you from accessing the good things, but it can also protect you from the bad things.
It also depends on the person who's eating the food and what they are eating it for. The stronger food matrix in whole-grain foods may be good for keeping blood sugar levels under control in a person with type 2 diabetes. However, this wouldn't be favourable for an endurance athlete trying to refuel during or in between training sessions.
You can choose to keep the food matrix "intact", naturally alter it yourself, or just remove it entirely. However, the state of the food matrix can actually determine how healthy it is, maybe just as much as the actual nutritional content of the food. So, understanding how it works and how to change it in your favour can be good for your nutrition and long-term health.
Food Matrix: The Good and the Bad
The good: whole foods first approach
The food matrix in whole foods can work in your favour to affect how well (and how quickly) you digest and absorb the nutrients from food. For example, the "actual" calorie content of nuts (i.e., what your body takes in and uses, called "metabolisable" energy) depends on how intact their food matrix is.
Put another way, 100 calories of whole almonds contain the same energy as 100 calories of pure almond butter (i.e., with no other ingredients). However, if you eat whole almonds, your body absorbs 22% fewer calories. That isn't mentioned on the back of the pack, is it?
How? Well, this is the food matrix in action. In whole almonds, a larger amount of fat remains trapped inside the food matrix and is not absorbed into your body. Whereas, if those same almonds are ground into butter, the food matrix is destroyed, meaning more fat is absorbed.
Something similar is seen when you compare some whole fruits to their fruit juices (e.g., orange and apple juice). The intact food matrix in the whole fruit slows down digestion, releasing sugar slowly into your bloodstream rather than all at once.[3]
Another example is dairy food. For years, doctors and dietitians recommended limiting full-fat dairy because of its saturated fat content. However, despite its saturated fat content, large studies kept finding that full-fat dairy products, particularly fermented dairy (e.g., cheese and yoghurt), did not meaningfully raise cholesterol.[4][5]
It seems that the fat in full-fat dairy, some of the calcium, saturated fat, protein and other substances bond and form their own unique food matrix in your gut, so not all of the saturated fat is absorbed by the body. Again, the food label says one thing, but what your body actually absorbs is another thing. This is the food matrix at work. And it has left a lot of doctors and dietitians scratching their heads.
The bad: The "collapse" of the food matrix in ultra-processed foods
One of the issues with ultra-processed foods is not just about the bad things that they contain, like added salt, sugar, fat or artificial ingredients, but it's also about the collapse and complete removal of the food matrix.
Big food companies use industrial processes to remove the food matrix and then recombine the raw ingredients back into soft, calorie-dense, tasty products that you can eat a lot of. When the food matrix is removed, you don't need to chew as much; the food is digested and absorbed more easily and quickly, and you don't get the "I'm full" signal. This means you can eat more of it without feeling as full.[6]
We have several other articles on what ultra-processed foods are, the health risks of eating too much of them and how to avoid them in your diet if you want to read more.
Is the food matrix always good? It's all about context
While preserving the food matrix is usually good for your health, there are some cases where removing or altering the matrix can be good. This is usually where your body needs a lot of nutrients very quickly.
For athletes, there may be certain times when they need to get nutrients into their bodies very quickly (e.g., protein, carbohydrate, caffeine). Powders, pills, drinks and gel products don't have a complete food matrix, which means the nutrients in them can pass through the stomach and gut easily and into the body quickly.
A long-distance cyclist wants to get the energy (carbohydrates) to the working muscles as quickly and easily as possible. They don't want parts of the food matrix overloading the digestive system while their muscles are working at full capacity.[7]
There may also be certain circumstances where removing or altering the food matrix can improve nutrition and health. For example, for people who want to gain weight, frail older adults, or people with gut health problems. For these people, the food matrix can be altered with simple food preparations and cooking methods to improve the digestion and absorption of some nutrients. [8]
How to Make Food Matrix Work in Your Favour: Practical Application
Sometimes you want to keep the food matrix, sometimes you want to remove it, and sometimes you may just want to alter it or partially remove it.


