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# Unplugging the Food Matrix for Nutrition and Human Health
- URL: https://www.alphabetguides.com/food-matrix/
- Published: 2026-09-20T08:00:41.000Z
- Updated: 2026-11-01T12:57:42.000Z
- Description: 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.
- Author: Dr. Robert Davies
- Tags: Diet & Nutrition, Health & Wellbeing, New Western Diet

summary 

- 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 in your gut. But it's not always good!
- Smart cooking techniques and preparation methods that alter the food matrix can sometimes improve nutrient uptake.

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](https://www.alphabetguides.com/an-apple-a-day-keeps-the-doctor-away-a-review/): 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 waythat 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. [\[1\]](https://pubmed.ncbi.nlm.nih.gov/30040431/?ref=alphabetguides.com) 

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](https://www.alphabetguides.com/fasting-and-diabetes/) 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. 

One hundred grams of whole almonds contain about 10% less "metabolisable" energy than roasted almonds, 12% less than chopped almonds, and 22% fewer calories than almond butter.[\[2\]](https://pubmed.ncbi.nlm.nih.gov/27713968/?ref=alphabetguides.com)

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.[\[3\]](https://pubmed.ncbi.nlm.nih.gov/6259919/?ref=alphabetguides.com) 

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.[\[4\]](https://pubmed.ncbi.nlm.nih.gov/26011901/?ref=alphabetguides.com)[\[5\]](https://pubmed.ncbi.nlm.nih.gov/28404576/?ref=alphabetguides.com) 

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** justabout 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](https://www.alphabetguides.com/appetite-and-body-weight/). This means you can eat more of it without feeling as full.[\[6\]](https://pubmed.ncbi.nlm.nih.gov/31105044/?ref=alphabetguides.com) 

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.

[What Are Ultra-Processed Foods? (And How to Spot Them)A guide to ultra-processed foods and the NOVA classification. Learn how to identify these products and make healthier choices without confusion.![](https://storage.ghost.io/c/69/dc/69dcec6d-c40d-40e8-823a-e4ec7bb45b10/content/images/icon/Logo--Square--1-54bf0a0f-fafc-48ab-b7d2-bfeed201623b.png)Alphabet GuidesDr. Robert Davies![](https://storage.ghost.io/c/69/dc/69dcec6d-c40d-40e8-823a-e4ec7bb45b10/content/images/thumbnail/photo-1761579339698-76489ea1bce8-413adaaa-788d-4f27-8649-65ea4011563b)](https://www.alphabetguides.com/ultra-processed-food-an-introduction/)

[The Health Risks of Ultra-Processed FoodsAn overview of ultra-processed foods and health. In this article we’ll look at the links to obesity, heart disease, and other health outcomes.![](https://storage.ghost.io/c/69/dc/69dcec6d-c40d-40e8-823a-e4ec7bb45b10/content/images/icon/Logo--Square--1-f6fde02b-38ec-41d6-bb9f-b12f326892b9.png)Alphabet GuidesDr. Robert Davies![](https://storage.ghost.io/c/69/dc/69dcec6d-c40d-40e8-823a-e4ec7bb45b10/content/images/thumbnail/photo-1688217170693-e821c6e18d72-99a008e2-f7d6-4105-bcf7-eb2afdf01479)](https://www.alphabetguides.com/health-effects-of-ultra-processed-foods-an-overview/)

[How to Avoid Ultra-Processed FoodA practical guide to reducing ultra-processed foods, offering strategies and flexible meal swaps that support healthier eating habits.![](https://storage.ghost.io/c/69/dc/69dcec6d-c40d-40e8-823a-e4ec7bb45b10/content/images/icon/Logo--Square--1-cdcc546c-0d11-48e3-aaf9-4fba96babdd4.png)Alphabet GuidesDr. Robert Davies![](https://storage.ghost.io/c/69/dc/69dcec6d-c40d-40e8-823a-e4ec7bb45b10/content/images/thumbnail/photo-1765850909380-2bdfc1c33422-8472f38b-99cd-4c44-8a34-3e54e44ad06b)](https://www.alphabetguides.com/how-to-avoid-upfs/)

### 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.[\[7\]](https://pubmed.ncbi.nlm.nih.gov/12617691/?ref=alphabetguides.com) 

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. [\[8\]](https://pubmed.ncbi.nlm.nih.gov/32806532/?ref=alphabetguides.com) 

---

## 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. 

### Strategy #1: Preserve the matrix

If your goal is to [lose fat, maintain a healthy body weight](https://www.alphabetguides.com/tag/fat-loss/), stop overeating, or keep your blood sugar and insulin levels steady, you should generally choose foods with an intact food matrix. 

1. Swap nut butters for whole nuts. Less energy is absorbed from whole nuts than nut butters, and you probably won't be able to eat as many calories from whole nuts in the first place.
2. Choose whole grains over processed or refined grains. Whole oats, brown rice, and quinoa have their matrix more intact than their refined alternatives. But even whole-grain flour products (e.g., breads or breakfast cereals) have had their food matrix pulverised.
3. Swap sugar-sweetened beverages for fruit juice, then swap fruit juice for whole fruit. A whole fruit contains more intact food matrix than just its juice does. But 100% fruit juice is also better than a sugar-sweetened artificial fruit drink, which has no food matrix at all.[\[9\]](https://pmc.ncbi.nlm.nih.gov/articles/PMC12800538/?ref=alphabetguides.com)

****Blending vs. Juicing:** Blending breaks down the physical food matrix while keeping the beneficial fibre intact, whereas juicing strips away the matrix and fibre entirely. 

### Strategy #2: Break or modify the matrix to improve nutrient absorption

Some key nutrients (like fat-soluble ones) in some foods are locked so tightly in the matrix that your body cannot release and absorb them. In this scenario, **lightly processing the food is favourable**.

1. Cook tomatoes and red peppers in olive oil. A nutrient found in tomatoes, called lycopene, is released from the food matrix when it is cooked in [olive oil](https://www.alphabetguides.com/superfood-olive-oil/), and more of it is absorbed by your body.[\[10\]](https://pubmed.ncbi.nlm.nih.gov/9209178/?ref=alphabetguides.com)[\[11\]](https://pubmed.ncbi.nlm.nih.gov/15927929/?ref=alphabetguides.com)
2. Soak and boil legumes to improve the absorption of their proteins and minerals.[\[12\]](https://pubmed.ncbi.nlm.nih.gov/36299246/?ref=alphabetguides.com)
3. Roast carrots, sweet potatoes and squash in [olive oil or canola oil](https://www.alphabetguides.com/canola-vs-olive-oil/) to help release and absorb their antioxidant and vitamin A content.
4. Lightly steam cruciferous vegetables (e.g., cabbage, kale and broccoli) and leafy greens. This will preserve their nutrients better than heavy boiling does, but it also makes them easier to eat.
5. Switch between eating raw and cooked vegetables. In some foods, cooking increases the availability of some nutrients, but decreases other nutrients. So, eat a mix of raw and cooked vegetables throughout the week to get full coverage.
6. Make the cooking liquid part of the dish. Instead of boiling your vegetables and then throwing the water down the drain (with the valuable nutrients in it), use that water as a stock to make soups, stews, curries, gravy or sauces.

### Strategy #3: Prioritise the food matrices that are good for your health

If you enjoy dairy foods, opt for fermented "solid" food matrices like hard cheeses or plain full-fat yoghurt. The live "good" bacteria, protein and calcium lattices can protect your cholesterol levels while providing a lot of nutrients (and flavour). 

Choose minimally processed over ultra-processed foods or ingredients. If you're going to buy processed foods, choose ones that retain coarse textures like stone-ground flours or steel-cut oats. These are generally better than food products that are made from fine-powdered or "reconstituted" products. 

---

## Bottom Line

The food matrix is there to remind us that nature packages nutrients intentionally; the foods we eat are not merely the sum of their parts. They are more than collections of molecules; they are themselves complex, structured, whole biological systems. If you want to make the food matrix work in your favour, some general rules are to: 

1. Keep whole foods as the default choice. We have teeth, digestive muscles, gut bacteria, and make our own enzymes and solvents for a reason; they are there to help us digest and absorb foods in their natural state.
2. But unlock nutrients where it makes sense. Cooking, chopping, soaking, and blending whole foods can increase the amount of nutrients we absorb.
3. In most cases, avoid products that "collapse" their food structures. Minimise your intake of ultra-processed foods, which are made of ingredients that have been stripped from their natural form, or in some cases are completely artificial.

We're not telling you to completely ignore the nutrition labels. But we also think that there are other important things to concentrate on. The physical structure of your food (the food matrix) is one of these things that barely gets a mention. By understanding how the food matrix works, you can take control of the things that you want (and don't want) in your body. 

---

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