10 Surprising Factors Preventing You From Losing Weight

Your “metabolic fire” is impacted by much more than just how much you eat and exercise. In this article, you’ll learn about ten key factors that affect energy balance and metabolism. When these factors are dialed in, you can optimize your energy balance and support a healthy body weight.

Body weight regulation is a priority for many of my clients, particularly many of my clients with Lyme disease and mold illness. Many of my clients come to me feeling very frustrated by their inability to lose weight or improve their body composition, despite doing seemingly everything “right” with their diet and exercise. While diet and exercise are crucial for supporting a healthy body weight, several other factors fly under the radar that significantly influence energy balance. In this article, we’ll take a look at ten factors that affect energy balance and metabolism beyond just diet and exercise (though you will see several sub-elements of diet and exercise discussed).

A Brief Overview of Energy Balance

In biology, energy homeostasis, also referred to as “energy balance,” is a process that involves the inputs that influence the difference between energy intake and energy expenditure. In other words, energy balance represents the relationship between “energy in” and “energy out.” Energy balance has crucial implications for regulating body weight (1); a positive energy balance indicates that you are consuming and absorbing more calories than your body is burning. A negative energy balance suggests that you are burning more calories than you are absorbing and consuming. A negative energy balance is a prerequisite for weight loss.

Simply put, energy balance is = calories in (energy input) – calories out (energy output)

For reference, an energy balance of 0 indicates that you have a balanced energy intake and expenditure; theoretically, this should result in a net weight gain of 0 lbs.

For weight loss, a negative energy balance of 300 kcal (Calories) per day works well for many people, promoting a weight loss of approximately 1 lb. every week. However, there are some people who may actually need to increase their calorie intake to lose weight! More on this below in the section titled “Insufficient Calorie Intake.”

Energy balance is a function of total energy expenditure (TEE), the number of calories burned by the human body in one day adjusted for the amount of physical activity one engages in, and the ingestion of metabolizable energy (aka food). TEE is a function of resting metabolic rate (RMR) (basal metabolic rate (BMR) is often used interchangeably with RMR) and of energy expended through the digestion and assimilation of food (“diet-induced thermogenesis,” or TEF) and through physical activity (“activity energy expenditure,” or AEE). TEF and RMR fluctuate over the day, according to the body’s circadian rhythm. TEF and AEE are modifiable through diet and exercise, respectively. Collectively, RMR and TEF contribute to approximately 80% of TEE.

It is well-known that TEE varies based on age, sex, body size, body composition, and genetics. However, numerous other factors impact TEE and that, when addressed, can shift the needle in terms of body weight, helping individuals overcome weight loss resistance.

While there is no easy way to measure TEE outside of a laboratory setting, though there are equations available that we can use to approximate energy expenditure and caloric energy needs. One equation that I frequently use in my clinical nutrition practice is the Harris-Benedict Equation, which calculates an approximate BMR; this value can then be multiplied by an activity factor to estimate energy needs for an individual.

10 Factors That Impact Energy Balance

In my research and clinical practice, I’ve found that body weight is impacted by far more than just the “calories in, calories out” model. So far, I’ve identified 10 key factors that affect energy balance and metabolism, outside of total calories and exercise.

Meal & Macronutrient Timing

It’s not just what you eat, but when you eat that affects your health. I previously wrote about the relationship between meal timing and health outcomes in my blog, How Meal Timing Affects Your Health. One of the main takeaways in that article was that eating most of your daily calories during daylight hours, as opposed to nighttime, aligns with our ancestral biology and appears to support optimal health. Our feeding and activity patterns are regulated by our circadian rhythms. Our circadian rhythms are initiated at the molecular level in virtually every cell of our bodies. More and more, we are learning how it behooves our health to live in accordance with our circadian rhythm.  (2)

What does meal timing have to do with your body’s energy balance? Well, it turns out that eating in accordance with our circadian rhythm (i.e., eating during a specific window of time, ideally during daylight hours) is associated with an increased TEF. (3) This means we can burn more energy during digestion when we eat according to our circadian rhythm; this eating strategy may support a negative energy balance and shift the needle on weight loss.

The timing of your intake of macronutrients (protein, carbohydrate, and fat) over the day may also affect your energy balance. Research suggests that eating an evening meal higher in fat and lower in carbohydrates is preferable to eating a high-carb dinner because our cells’ carbohydrate utilization as an energy substrate is blunted in the evening. When cells aren’t able to efficiently take up glucose (from carbohydrates), a metabolic “traffic jam” can occur, with downstream effects on body weight. Conversely, you may want to eat more of your carbohydrates with your morning meal, when insulin sensitivity is at its highest.

In my article, How Meal Timing Affects Your Health, I discussed the problems posed by nighttime snacking. One of those problems is that nighttime snacking reduces fat oxidation, or your body’s ability to burn fat for fuel. Over time, blunted fat oxidation at night could disrupt overall energy balance. (4)

Last but not least, the repartition of calorie intake throughout the day may also impact energy balance. (5) Preliminary research suggests that eating most of one’s daily calories earlier in the day may be optimal for weight control due to circadian variations in energy expenditure, with RMR and TEF appearing to be higher in the morning than at night. This means the body burns more calories carrying out basic metabolic processes and digestion in the morning than at night. (6, 7, 8) The studies we have available also suggest that the human body burns fewer calories during the biological night, so eating large quantities of food at night may impair energy balance and make one more prone to weight gain. Front-loading your calories earlier in the day may thus be better from an energy balance perspective.

Please note that our understanding of meal timing and its impact on energy balance is still in its infancy, so the ideas discussed here are subject to change as our understanding of this science evolves.


Inflammation occurs in the body when a physical stimulus triggers an immune reaction. Acute inflammation occurs in situations such as when you get a cut or a bug bite; the area around the cut or bug bite becomes red and inflamed as your immune system begins the process of repairing the damage. On the other hand, chronic inflammation is a less obvious process elicited by daily inputs that trigger a low-level immune response, such as the consumption of a processed diet. Research indicates that inflammation in parts of the body, such as the hypothalamus and adipose tissue, may disrupt energy balance and contribute to fat gain. (9) Getting to the bottom of what is triggering inflammation in your body, be it a tickborne infection, sleep deprivation, or toxin exposure, is essential for resolving inflammation and a healthy energy balance.

Thyroid Hormones

Thyroid hormone impacts all of the components of TEE, including RMR, TEF, and AEE. Activation of thyroxine (T4) to the active thyroid hormone triiodothyronine (T3) in peripheral tissues is a crucial mechanism by which thyroid hormones impact metabolism and energy balance. Low levels of T3 thus reduce total energy expenditure and may promote a positive energy balance. (10) Optimizing your thyroid health is essential for optimizing your energy balance. Addressing thyroid health starts with doing a complete thyroid panel and optimizing your intakes of thyroid-supporting nutrients.

Insufficient Calorie Intake

A hypocaloric diet is defined as a diet characterized by a low number of calories. While it may seem counterintuitive, eating a hypocaloric diet for an extended time may actually impair energy balance and promote weight plateauing or weight gain by decreasing RMR! When someone consumes a diet that is very low in calories, the body engages evolutionary mechanisms to preserve body weight by downregulating RMR. (11)

The point here is that eating a low-calorie diet is NOT the way to go for sustainable weight loss. A reduced RMR reduces TEE and maybe a leading reason why dieting does not work for sustainable weight loss. Based on this science, I do not recommend low-calorie diets to my clients. While we can reduce caloric intake to a degree to jump-start weight loss, there is a certain threshold below which it is unwise to reduce calorie intake further.


Sleep is an underappreciated but critical regulator of energy balance. Insufficient sleep leads to increases in energy intake that outweigh any increase in energy expenditure associated with sustained wakefulness, resulting in a positive energy balance and an increased risk of weight gain. (12) Optimizing your sleep routine is thus one of the best things you can do for your energy balance and countless other aspects of your health!


Exercise can assist with creating a negative energy balance, to a degree. Exercise burns calories, which can promote a negative energy balance, provided that caloric compensation for exercise doesn’t exceed the calories burned. Exercise also supports the growth of skeletal muscle (also referred to as “lean body mass” or “fat-free mass”), which increases the body’s energy expenditure. (13) There is also an after-effect of exercise on RMR; exercises induces a significant increase in RMR for approximately two hours after exercise and a smaller but more prolonged effect for up to 48 hours post-exercise. This phenomenon is called excess post-exercise oxygen consumption; however, it only boosts TEE minimally. (14)

However, our bodies appear to have some adaptive mechanisms in place that limit just how much energy we can burn through exercise over a sustained period. The concept of “constrained total energy expenditure” demonstrates that total energy expenditure (TEE) is positively correlated with activity at lower exercise levels, yet as exercise levels increase TEE plateaus. This means that simply doing more exercise over time may not yield benefits for energy balance because our bodies adapt to the higher level of physical activity by reducing the number of calories we burn performing that activity! (15) However, please do not take this as a suggestion to stop exercising! Exercise offers numerous health benefits above and beyond energy balance; I consider exercise to be an essential “nutrient” equally as important as diet for sustaining a healthy mind and body.

Non-Exercise Physical Activity (NEPA)

Non-exercise physical activity (NEPA), sometimes referred to as non-exercise thermogenesis or NEAT, is defined as the energy our bodies expend for non-exercise physical activities such as walking, maintaining our posture (16), house cleaning, performing yard work, and even fidgeting! A low level of NEPA is associated with increased body fat mass. Engaging in more NEPA throughout your day may support a healthy energy balance.

Taking the stairs, working at a standing desk, and “active sitting” (such as sitting on a physioball chair rather than a regular chair) are several ways to increase your daily NEPA.

The postural muscles that are engaged when working at a standing desk contribute to non-exercise physical activity (NEPA). NEPA is an essential, but often overlooked, component of the energy balance equation.

The postural muscles that are engaged when working at a standing desk contribute to non-exercise physical activity (NEPA). NEPA is an essential, but often overlooked, component of the energy balance equation.

Environmental Toxins

Anthropogenic pollutants, or manmade chemicals, are abundant in our environment. The EPA has more than 85,000 manmade chemicals listed in its inventory of toxic substances that fall under the Toxic Substances Control Act but does not know how many of those chemicals currently use today. Preliminary research suggests that some of the chemicals circulating in our environment may interfere with energy balance and promote body fat gain.

In the POUNDS study, 621 overweight and obese participants went through a calorie-restricted diet to induce weight loss. The participants were followed for 2 years. The researchers ultimately found that participants with higher baseline levels of perfluoroalkyl substances (PFAS), chemicals used in nonstick pans, food packaging, and waterproof jackets, experienced a significantly higher weight regain rate after their initial weight loss. Higher baseline levels of PFAS were also associated with greater reductions in RMR during weight loss in women but not men, indicating a disruption in the female subjects’ energy balance. PFAS may exert these effects by acting as endocrine disruptors or compounds that interfere with the body’s endocrine (hormonal) systems. (17) This research suggests that manmade chemicals interfere with energy balance and body weight regulation. The detoxification of these chemicals may be an essential step for supporting a healthy energy balance and body weight.

Gut Microbiota

The microbes in your gut experience their own circadian rhythms, leading to time-specific compositional and functional microbial profiles throughout a 24-hour period. The circadian activities of gut microbes impact glucose intolerance and fat gain, presumably due to changes in energy balance. (18) Eating in a way that syncs with your circadian rhythm (as discussed above) and supporting your gut microbes’ overall health with a whole foods diet are two ways to promote a gut microbiota conducive to healthy energy balance.

Differences in Absorptive Efficiency in the Gut

Finally, differences in your digestive tract’s absorptive capacity may also impact your energy balance. The metabolizable energy of a diet is the difference between the total amount of energy in ingested substrates (food) and the energy losses found in stool and urine. Research indicates that absorptive efficiency in the gut varies due to several factors, including the composition of the gut microbiota, how food is prepared, and overall diet composition.

  • Certain gut microbes, such as Methanobrevibactor smithii (implicated in methane-predominant SIBO or “intestinal methanogen overgrowth” or IMO) are exceptionally efficient at breaking down dietary carbohydrates, allowing your gut to absorb more caloric energy from ingested carbohydrates.

  • Intact plant foods, such as whole nuts and vegetables, contain plant cell walls that protect the cell contents (lipids and carbohydrates) from digestive enzymes in the gut. These intact whole foods thus offer less metabolizable energy to the gut than more processed versions of these foods, such as nut butter or applesauce, for example. Mastication breaks down intact plant foods to a degree, but to a lesser extent than does mechanical “pre-mastication” using food processing techniques.

  • The overall composition of one’s diet also impacts the absorptive efficiency of the gut. A diet high in fiber reduces the absorption of some nutrients, impacting absorptive efficiency.

Along these lines, a person who has higher levels of Methanobrevibacter smithii, a microbe that increases energy harvest in the gut (19), eats foods that have been mechanically predigested (such as processed foods), and eats a diet low in fiber and protein may absorb more energy from ingested food that someone with lower levels of M. smithii and an unprocessed diet rich in fiber and protein.

As you can see, energy balance is not merely a matter of eating less and exercising more; it hinges on numerous variables that work synchronously to affect how your body absorbs and utilizes caloric energy. Addressing all of these factors, rather than just cutting calories and plugging away at exercise, is essential for promoting a healthy, sustainable energy balance.

Are you dealing with Lyme disease or mold illness and struggling to lose weight? Consider working with me! I am currently accepting new clients in my clinical nutrition practice. If you’re interested in diving deep into improving your nutrition and health by working one-on-one with me, reach out to me here to schedule your discovery call. The discovery call will allow us to meet and talk together to decide if my nutrition services are the right fit for your needs. I look forward to connecting with you!

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