Have you ever experienced mental fatigue? Hard to focus, getting distracted, re-reading something couple of times just to make sense of it? Being overwhelmed with small decisions and tasks or relaying on coffee and snacks to keep you ‘awaken’ and productive, especially in the afternoon?
Low energy, physical fatigue and difficulty in waking up in the morning are very common with under-active thyroid but lack of mental clarity is a thing too. You are not crazy, brain fog is real. Let’s take a look what is causing it and 5 things you can do to improve it.
Nutrients deficiencies, food intolerances and simply eating wrong foods
One of the main contributors to brain fog is your diet. What we eat everyday has a big impact on our body. If you eat wrong foods each day, nothing will happen overnight but after a while you may start experiencing range of “unexplained” symptoms.
Lack of vitamin D and B12 are the major nutrient deficiencies linked with brain fog. I know that you hear about vitamin D everywhere. Yes – low vitamin D levels can impair your cognitive function and the severe prolonged deficiency can even lead to depression. B12 on the other hand apart from being known as “energy” vitamin is also needed for brain cell communication. It’s required for neurotransmitter synthesis too, in other words you need B12 to think sharp and clear. However, I would avoid B12 fortified products like cereals or plant milks. The form of B12 in those usually is very poor and not well absorbed. Instead, chose some of B12 rich foods like:
- Shellfish, such as mussels and clams
- Dairy products
- Poultry products, such as chicken, turkey, and eggs
- Nutritional yeast
Or if you know you have problem with methylation, go for methylated B vitamin supplement. You can read more about hidden vitamin deficiency here and what is the most accurate test to detect vitamin B12 deficiency early – check “How you can be deficient in vitamin B12 without knowing” section.

Food intolerances and brain fog
Have you ever experienced feeling sleepy or sluggish after your meal? Well, food intolerances and poor histamine breakdown could be one of the reasons. Food intolerances are linked with leaky gut. What usually is damaging and causing leaky gut is of course your diet. However, there are some other factors contributing to it like excess alcohol consumption, chronic stress and range of various toxins. From pesticides in the food, environmental pollutants to heating food in plastic containers and drinking from plastic bottles. Everything mentioned can throw your gut microbiome out of balance.
Histamine is interesting one in terms of gut health. If you have imbalance between good and bad bacteria or simply too much bacteria, they can release a lot of histamine. Excess histamine can cause brain fog. If the problem lies with bacteria overgrowth, not poor histamine breakdown itself, then low FODMAP diet works quite well as it helps to starve the “unwanted” bacteria.

Two things you need to know about your gut:
What you need to know about your gut are two things that are not related to digestion:
80% of your immune system is in your gut and what more relevant on this topic is that
Your gut is your “second brain”
There is strong evidence that gut microbiota has an important role in communication between the gut and your brain cells. It interacts with your central nervous system by regulating brain chemistry and influencing neuro-endocrine systems associated with stress response, anxiety, cognitive function and memory. Your gut also produces neurotransmitters like serotonin – your happy hormone.
Improve your gut to get rid of brain fog and gain mental clarity again.
If you want to re-gain mental clarity, be more productive and better at analysing and making decisions, take care of your gut. It’s mind blowing how our body works. I saw decent amount of people in my practice with significant improvements in the mood just by working on their gut. Additionally, including the right strain of probiotics on the top of that can be game changing.

How underactive thyroid affects your gut and causes brain fog?
With underactive thyroid everything in your body slows down. Not only your metabolism, energy production and detoxification capabilities but also how effectively your body is “cleaning up your gut”. Or if you prefer fancy name, how your migrating motor complex is working. Hypothyroidism impairs your gut motility and how quickly the food is processed and “pushed” through your system. Underactive thryoid and poor gut motility increases risk of SIBO (small intestine bacteria overgrowth). If you have too much bacteria growth in the wrong place (in the small intestine instead of your large intestine), it will contribute to the impaired gut – brain communication on the top of other symptoms like gas, bloating and feeling of fullness without eating. What’s more, taking levothyroxine (common medication to manage low thyroid) increases risk of developing SIBO significantly.
Hypothyroidism and Hashimoto’s natural treatment
That’s why I always encourage women to try natural treatment for hypothyroidism before taking medication as with the right nutrients and the diet you can naturally restore your thyroid function without side effects of the medication. The same with Hashimoto’s, natural treatment for Hashimoto’s that addresses the root cause is way more efficient and can help you resolve the symptoms that Levothyroxine can’t.

Hypothyroidism and low stomach acid levels
Another important thing to note is that low thyroid function decreases stomach acid levels. That means that you won’t be absorbing nutrients from food well which brings us to the first point where we talked about nutrient deficiencies and brain fog. Vitamin B12 absorption from food is dependent on intrinsic factor (produced by cells in your stomach). Intrinsic factor can be produced only in presence of enough stomach acid. “You are what you absorb” is not another slogan, it’s actually very true and important. Not only what we eat but how and if we absorb it well. Here is a quick guide how to increase your stomach acid levels
Hashimoto’s, excess inflammation and brain fog
An unmanaged autoimmune condition causes chronic inflammation. In Hashimoto’s, the chronic inflammation is slowly damaging cells and thyroid tissue. What many people don’t realize is that chronic inflammation affects brain too. On a cellular level, brain fog is believed to be caused by high levels of inflammation and changes to hormones that determine your mood, energy and focus. Chronic inflammation slows down the speed at which your brain operates, making it less efficient. It can cause your brain cells to degenerate or age more quickly.
5 things you can do to improve your brain fog:
As you can see a lot of things can contribute to the brain fog. Defining the major contributor is the key if you want to see improvements quickly but at the same time you feel implementing everything at once is just too much. Always target what is causing the most of the damage first. Additionally, Hashimoto’s can exacerbate your symptoms due to inflammation so managing your inflammation is also important.

Here are 5 most important things you can do to improve brain fog:
- 1. Improve your gut microbiome and instead of stocking on probiotics and other supplements, first, remove the main irritants like sugar, alcohol, gluten and processed foods in general. For a lot of people removing gluten is a big game changer.
- 2. Reduce intake of highly inflammatory vegetable oils. Swap sunflower, rapeseed, canola, corn or soybean oil with coconut oil and omega 3s. Coconut oil has powerful antimicrobial and anti-fungal properties that can help reduce bad bacteria overgrowth in your gut. Omega 3s on the other hand have great anti-inflammatory benefits. Oily fish is good source of omega 3. Check my other post here to find out how to choose the right fish as fish is unfortunately highly contaminated with heavy metals. Toxic overload can affect your gut and also impair your thyroid function.
- 3. Make sure you eat whole food, rich in nutrients, especially B12, vitamin C, Vitamin E and magnesium.
- 4. Get more exercise. Ideally outdoors. Exercise increases oxygen to the brain, improves memory and concentration, and can protect your brain from stress and inflammation. Exercise also causes the release range of chemicals that have beneficial effect. One of them that you may be familiar are endorphins. They help to repair and rejuvenate the brain. Try to engage in some type of exercise or movement, best choose something that you enjoy.
- 5. Get enough sleep, rest and also let your digestive system rest. When you eat too much to often there is no time for your body to do the “clean up”. Aim for at least 12h fast between dinner and breakfast. It will also help to regulate your blood sugar and insulin which again is linked with inflammation. You can read more about impact of your insulin on your body here.
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