Root Causes
November 26, 2025

Why Hashimoto’s Patients Still Struggle With Symptoms Despite Taking Thyroid Hormones

WRITTEN BY
Dr Dimitris Tsoukalas, MD, PhD
Chief Medical Advisor

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Why Hashimoto’s Patients Still Struggle With Symptoms Despite Taking Thyroid Hormones

Hashimoto's disease causes symptoms that burden patients' quality of life, even when tests show the thyroid is functioning normally.
Metabolic disorders like insulin resistance and micronutrient deficiencies often go undetected by standard laboratory tests, burdening patients' health for years.
Patients with Hashimoto's disease struggle with low energy, muscle pain, weight gain, and mood swings – symptoms that make everyday life difficult.

Many people with Hashimoto's thyroiditis don't feel well, even when their hormone tests are normal. Common laboratory tests often miss deficiencies and metabolic disorders, which can go undetected for years.

Hashimoto's disease is an autoimmune condition where the immune system mistakenly attacks the thyroid gland, producing antibodies that gradually destroy it.

Deficiencies and metabolic disorders cause thyroid dysfunction, leading to the most common symptoms patients experience: fatigue, low energy, weight changes, digestive issues, mood disturbances, and brain fog.

Patients Often Feel Unwell Despite Normal Blood Tests

Recent evidence shows that many patients don't feel well and report reduced quality of life, even when their blood tests are normal [1].

The most common problems patients face include:

  • Fatigue
  • Weight gain despite eating less
  • Constipation
  • Difficulty concentrating
  • Mood swings

Higher antibody levels have been linked to reduced quality of life in Hashimoto's patients, even when thyroid function appears normal.

Patients report that the disease negatively affects their social life, perceived health, sex life, and body image [2][3].

Why the Thyroid Becomes Dysfunctional

The thyroid gland constantly regulates metabolism, specifically, how fast metabolic processes occur. It adapts metabolism to daily changes in external temperature, energy needs, digestion, and mood.

When we climb stairs or exercise, the thyroid increases its activity and speeds up metabolism. It does the same in cold conditions, when we face stress or challenges, and when we feel happy or excited. On the other hand, during relaxation, sadness, or heat, thyroid decreases its activity and slows metabolism.

Reduced thyroid function and the resulting metabolic slowdown explain why hypothyroidism causes fatigue, cold intolerance, low mood, and weight gain.

On the other hand, hyperthyroidism causes the opposite: hyperactivity, weight loss, rapid heartbeat, heat intolerance, and other signs of increased metabolism..

Low vitamin D and selenium levels, iodine deficiency, exposure to endocrine-disrupting industrial chemicals, and certain medications impair proper thyroid function.

We also know that metabolic syndrome and insulin resistance are directly linked to thyroid dysfunction.

Individuals with thyroid dysfunction have an increased risk of insulin resistance and metabolic syndrome, disordered lipid metabolism, increased body weight, and hypertension, which together significantly raise cardiovascular risk.

Why Preserving Even Partial Thyroid Function Is Critical

The thyroid gradually becomes overwhelmed as it tries to activate a metabolism that isn't functioning properly.

At this point, exogenous hormone administration is a vital tool that can improve the clinical picture and the patient’s quality of life.

However, adjusting medication a few times per year cannot simulate the continuous and precise regulation carried out by the human body, with responses occurring within seconds.

We have found in our clinical experience that even when the gland is underactive by up to 80%, this deficit can be fully compensated with hormone replacement, without negatively affecting quality of life.

The remaining 20% of thyroid function is sufficient to support a large part of the normal metabolic adaptations to everyday demands, allowing for a very good quality of life.

For this reason, it is crucial to do everything possible to preserve any residual function of the gland, as it enables the body to adapt metabolically to these changes.

Identifying and correcting the body’s deficiencies and metabolic disorders that contributed to the development of thyroid disease is a central component of managing autoimmune thyroid conditions.

Deficiencies and Metabolic Disorders in Hashimoto’s Disease

Hashimoto’s disease has a significant metabolic background.

Thyroid disorders affect metabolism, but the reverse also occurs: metabolic disorders affect thyroid function.

Insulin resistance, stress, vitamin D deficiency, and low metabolic rate are the main factors that burden the thyroid.

In combination with deficiencies in vitamins, antioxidants, and minerals (selenium, zinc, magnesium), these factors lead to the development of the disease and negatively affect the course of patients’ health.

If the above factors are not addressed, treatment cannot be effective and the patient will continue to experience symptoms that make daily life difficult and worsen quality of life.

Metabolic factors that burden Hashimoto’s disease and contribute substantially to the symptoms patients experience are:

1. Reduced energy production by the body

This occurs due to dysfunction of the organelles that produce energy in cells [4][5][6].

2. Insulin resistance

This refers to the reduced responsiveness of cells to insulin. Elevated insulin levels block fat burning, increase hunger, and exacerbate chronic inflammation [7][8][9].

3. Micronutrient deficiencies

Deficiencies in vitamin D, selenium, magnesium, B vitamins, and antioxidants are common in people with Hashimoto’s thyroiditis. They impair immune function, worsen autoimmunity, and negatively affect metabolism [10][11].

4. Gut microbiome disturbances

Changes in the body's microbiome contribute to the development of autoimmune diseases and affect mood and hormone function [12][13].

5. Disorder in the body’s ability to manage inflammation

Hashimoto’s disease is a chronic inflammatory condition. The immune system mistakenly attacks the thyroid; immune cells and antibodies against the gland destroy thyroid tissue and cause inflammation.

Deficiencies in omega-3 fatty acids and impaired regulation of inflammation and tissue repair worsen the severity and progression of autoimmune diseases.

Poor inflammatory control affects the entire body, leading to chronic pain, fatigue, sleep disturbances, fluid retention, drowsiness, and reduced mental clarity [14][15][16][17].

To substantially improve the clinical picture and alleviate symptoms, care for Hashimoto's disease must include both thyroid hormone regulation and the identification and correction of accompanying deficiencies and metabolic disorders [7–16].

Comprehensive Blood Testing for Detecting Metabolic Imbalances in Hashimoto’s

Metabolic disorders can be identified and addressed through comprehensive blood testing that evaluates a wide range of biomarkers related to metabolism, hormones, inflammation, and nutrient status.

This approach detects metabolic disorders associated with the onset, course, and manifestation of Hashimoto's thyroiditis.

An individual's metabolic status is a key risk factor for the disease development and progression.

This approach differs from standard laboratory testing. It uses broad, integrated panels that provide a detailed overview of how different body systems function and interact, rather than analysing a few biomarkers in isolation.

These comprehensive blood panels identify specific deficiencies and metabolic imbalances, making the management and prevention of autoimmune and chronic diseases more targeted and effective.

Indicators Identified Through Kyma’s Comprehensive Lab Testing

Comprehensive blood panels can identify metabolic disturbances that promote the development and manifestation of Hashimoto’s disease, including:

1. Micronutrient deficiencies

Deficiencies in vitamin D, vitamin C, selenium, zinc, antioxidants, and omega-3 fatty acids are associated with deterioration of immune system function, the occurrence of inflammation, and overall health status in patients with Hashimoto’s [18][19].

2. Difficulty metabolising simple sugars

Patterns in blood glucose, HbA1c, triglycerides, and related markers can indicate reduced capacity to metabolise simple sugars. Excess intake beyond what each body can handle promotes inflammation and is an important indicator of disease course [15][22][23].

3. Insulin resistance

Insulin acts as a suppressive factor on thyroid function. Elevated insulin levels also disrupt immune function, exacerbate autoimmunity, and accelerate thyroid destruction [15][22][23].

4. Fatty Acid Metabolism

The ratio between omega-3 and omega-6 fatty acids is a crucial indicator of the body's ability to manage inflammation and regulate the immune system's normal response.

5. State of the Microbiome

Alteration of the microbiome is linked to impaired immune system function and the ability to distinguish between its own tissues and external elements, such as pathogens and viruses.

6. Thyroid Function

A complete assessment of TSH, Free T4, and Free T3 provides a direct picture of how effectively the thyroid produces and converts hormones. These markers reveal how well the gland meets the body's metabolic demands and help identify reduced hormone production and impaired conversion of T4 to the active hormone T3.

7. Thyroid Antibodies

Elevated anti-thyroid peroxidase (anti-TPO) and anti-thyroglobulin (anti-TG) antibodies reflect autoimmune activity and correlate with disease severity and progression risk.

8. Liver, Kidney and Cardiovascular

These tests assess organ function and cardiometabolic risk factors that often coexist with Hashimoto’s (e.g. dyslipidaemia, hypertension, fluid retention). They help distinguish thyroid-related symptoms from other causes and help reduce long-term risk.

Modern Approaches to Hashimoto's Thyroiditi's Care

Modern care for Hashimoto's disease focuses on identifying and correcting the deficiencies and metabolic disorders that led to the development of the disease. This approach restores normal function and maintains the body's optimal metabolic state.

In our clinical experience with patients diagnosed with Hashimoto’s disease, targeted interventions guided by comprehensive laboratory testing can lead to:

  • Improvement in the course of the disease by halting further destruction of the thyroid gland.
  • Preservation and enhancement of the remaining thyroid function, which allows the body to adapt metabolically to the continuous demands of everyday life, thereby supporting a very good quality of life.
  • Gradual reduction in autoantibody levels.
  • Reduction in fatigue and increase in energy levels.
  • Improvement in mood and a reduction in pronounced emotional fluctuations related to impaired thyroid function.
  • Reduced risk of damage to other organs and of developing additional autoimmune diseases.
  • Improved metabolism and achievement of a healthy body weight.
  • Improved response to medication.

It typically takes 6–8 months to achieve a meaningful change, around one year for the body to stabilise at a better level of functioning, and approximately two years to achieve optimal results.

As the body corrects deviations from optimal functioning, it reactivates normal metabolic processes – and its needs change accordingly.

When a personalized care plan is implemented, changes occur simultaneously across multiple metabolic pathways. These must be identified and supported appropriately for recovery to continue. Without this support, the body's natural healing processes may stall, significantly delaying health improvements.

In our clinical experience, correcting vitamin and micronutrient deficiencies, supporting healthy metabolism, and normalising body weight can significantly improve both the course of Hashimoto's and patients' quality of life – shifting the trajectory from constant deterioration to continuous improvement.

Early intervention with this type of supportive care is crucial for stabilizing and improving the condition over time.

Have questions? Schedule a call with a Kyma advisor.

References

[1] Persisting symptoms in patients with Hashimoto’s disease despite normal thyroid hormone levels: Does thyroid autoimmunity play a role? A systematic review  Karelina L. Groenewegen et al. J Transl Autoimmun. 2021

[2] Is Thyroid Autoimmunity per se a Determinant of Quality of Life in Patients with Autoimmune Hypothyroidism?  Watt T et al. European Thyroid Journal 2012

[3] Is thyroid autoimmunity itself associated with psychological well-being in euthyroid Hashimoto's thyroiditis?  Mehmet Muhittin Yalcin et al. Endocr J . 2017.

[4] Enhanced oxidative stress in Hashimoto's thyroiditis: inter-relationships to biomarkers of thyroid function.Rostami R1, Aghasi MR, Mohammadi A, Nourooz-Zadeh J. Clin Biochem. 2013 Mar

[5] Selenium involvement in mitochondrial function in thyroid disorders. Monica Livia Gheorghiu & Corin Badiu. Hormones 2020.

[6] Bioenergetic Aspects of Mitochondrial Actions of Thyroid Hormones  by Federica Cioffi  et al. Cells 2022

[7] Association between thyroid hormones and insulin resistance indices based on the Korean National Health and Nutrition Examination Survey  Yun Mi Choi et al. Nature -Scientific Reports (2021)

[8] Introducing the thyroid gland as another victim of the insulin resistance syndrome. Jorge Rezzonico et al. Thyroid 2008. https://pubmed.ncbi.nlm.nih.gov/18346005/

[9] Changes in Glucose-Lipid Metabolism, Insulin Resistance, and Inflammatory Factors in Patients With Autoimmune Thyroid Disease Yi Lei et. al. J Clin Lab Anal . 2019

[10] Correlation Between Hashimoto's Thyroiditis-Related Thyroid Hormone Levels and 25-Hydroxyvitamin D Guanqun Chao, Yue Zhu, Lizheng Fang. Front Endocrinol (Lausanne). 2020 Feb.

[11] Multiple Nutritional Factors and the Risk of Hashimoto's Thyroiditis Shiqian Hu, Margaret P Rayman. Thyroid . 2017 May.

[12] Gut microbiota and Hashimoto's thyroiditis  Camilla Virili et al. Rev Endocr Metab Disord. 2018

[13] Association Between Gut Microbiota and Autoimmune Thyroid Disease: A Systematic Review and Meta-Analysis  Boshen Gong, et al. Front. Endocrinol., 17 November 2021

[14] An update on the pathogenesis of Hashimoto's thyroiditis  A P Weetman et al.

[15] Targeted Metabolomic Analysis of Serum Fatty Acids for the Prediction of Autoimmune Diseases Dimitris Tsoukalas, Vassileios Fragoulakis, Evangelia Sarandi et. al. Frontiers in Molecular Biosciences, Metabolomics (6), November 2019.

[16] Nutritional Management of Thyroiditis of Hashimoto Yana Danailova et al.