By Stephanie Thompson, DNP, APRN, FNP-BC | Lake Town Wellness

There’s nothing quite as frustrating as waking up in the middle of the night, staring at the ceiling, and watching the clock tick toward morning. If you’ve found yourself consistently jolting awake around 3 AM, you’re definitely not alone—and no, it’s not just bad luck or that cup of coffee you had at lunch.

As a functional medicine provider, I see this pattern all the time. What surprises most of my patients is that these middle-of-the-night awakenings often aren’t about sleep at all—they’re clues about what’s happening beneath the surface.

Your Body Doesn’t Wake You Up for No Reason

When you wake up at the same time night after night, your body is trying to communicate something. Think of it like an internal alarm system that’s detecting an imbalance somewhere. The key is learning to interpret what it’s telling you.

Here are three common culprits I investigate with my patients:

Blood Sugar Instability

This is probably the most overlooked cause of nighttime waking that I see in my practice. Here’s what happens: if your blood sugar drops too low while you’re asleep, your body perceives it as an emergency. It releases cortisol and adrenaline to bring your glucose back up—and suddenly you’re wide awake at 3 AM with a racing heart and maybe even some anxiety.

You don’t have to be diabetic for this to happen. I see this frequently in patients with insulin resistance or those who eat a carbohydrate-heavy dinner without enough protein or fat to stabilize their blood sugar through the night.

Signs this might be you: You wake up feeling wired, anxious, or suddenly hungry. Sometimes you notice your heart beating faster than it should.

Your Liver Is Working Overtime

In Traditional Chinese Medicine, the hours between 1-3 AM are associated with liver function. Modern research actually supports this connection—your liver does a significant amount of its detoxification work during sleep, particularly in those early morning hours.

When your liver is overburdened—from processed foods, alcohol, medications, or the environmental toxins we’re all exposed to daily—it can struggle to keep up with its workload. The result? Your sleep gets disrupted right during peak liver activity.

Signs this might be you: You feel groggy or unrested even after a full night’s sleep. You may have digestive issues, skin problems, or difficulty tolerating fatty foods.

Cortisol Rhythm Disruption

Your stress hormone, cortisol, is supposed to follow a predictable pattern: highest in the morning (to help you wake up) and lowest at night (to help you sleep). Chronic stress, inflammation, or irregular schedules can throw this rhythm completely off track.

When your cortisol pattern gets inverted or spikes at the wrong times, it creates a biochemical environment that makes deep, restorative sleep nearly impossible.

Signs this might be you: You feel “tired but wired” at bedtime. You get a second wind late in the evening. Mornings are brutal no matter how much sleep you get.

What Actually Helps

Here’s the good news: once you identify what’s driving your sleep disruption, there are practical steps you can take.

For Blood Sugar Support

Consider how you’re structuring your evening meal. Including protein and healthy fats at dinner—and potentially a small protein-rich snack before bed—can help stabilize your blood sugar overnight. Think cheese with apple slices, a handful of nuts, or some Greek yogurt.

I also recommend limiting refined carbohydrates and sugars in the hours before bed. That bowl of cereal or late-night cookie might be contributing to your 3 AM wakeups.

For Liver Support

Focus on foods that naturally support liver detoxification: cruciferous vegetables like broccoli, Brussels sprouts, and cabbage; beets; garlic; and turmeric. These foods help activate the enzymes your liver needs to do its job efficiently.

Reducing your toxic load matters too—paying attention to what you’re putting on your skin, what you’re cleaning your house with, and how much alcohol you’re consuming.

For Cortisol Balance

This one requires addressing the root cause: your stress response. I know that sounds simple, but it’s often the hardest piece to tackle. Practices like meditation, breathwork, or gentle yoga before bed can genuinely help lower cortisol levels.

Consistency matters more than you might think. Going to bed and waking up at the same times—even on weekends—helps train your body’s internal clock.

The Mineral Connection

Something I often find in patients with persistent sleep issues is mineral deficiency. Minerals like magnesium, zinc, and potassium play crucial roles in blood sugar regulation, stress response, and the production of sleep hormones like melatonin.

Our modern diets and depleted soils make it difficult to get adequate minerals through food alone. This is one area where targeted supplementation can make a noticeable difference.

I recommend LDA Trace Mineral Complex — a comprehensive trace mineral supplement featuring Albion® chelated minerals for optimal absorption. It supports blood sugar stability, liver detoxification, and healthy cortisol rhythm in just one capsule daily.

When to Dig Deeper

If you’ve tried the basics—better sleep hygiene, stress management, dietary changes—and you’re still waking up at 3 AM, it might be time to look under the hood with some functional testing.

At Lake Town Wellness, we use advanced testing to identify root causes that basic labs often miss. Things like:

• Comprehensive metabolic panels to assess blood sugar regulation
• Cortisol rhythm testing to map your stress hormone patterns
• Nutrient testing to identify specific mineral or vitamin deficiencies
• Gut health analysis, since gut dysfunction often drives systemic inflammation

Your 3 AM wakeups aren’t random—they’re data. The question is whether you’re ready to listen to what your body is trying to tell you.

Stephanie Thompson is the founder of Lake Town Wellness in Heber Springs, Arkansas, where she combines traditional primary care with functional medicine to help patients find answers when conventional approaches fall short. If you’re ready to get to the root of your health concerns, schedule a consultation to discuss how functional medicine might help.