How Trauma Affects the Brain—and How to Heal It

Trauma changes the brain—but it doesn’t have to define it. Whether from a single event or long-term stress, trauma reshapes how the nervous system processes danger, emotion, and memory. Over time, this constant state of alert can lead to anxiety, fatigue, emotional numbness, and physical symptoms that make it hard to feel safe in your own body.

At our practice, trauma recovery begins with understanding what’s happening inside the brain. Using a science-based, integrative psychiatry approach, we help patients calm overactive stress circuits, restore emotional regulation, and rebuild resilience. This process often combines functional medicine testing, nutritional and hormonal support, and therapies like EMDR, DBT, and somatic work to help the body and brain reconnect.

Healing from trauma isn’t about erasing the past—it’s about teaching the brain and body that safety is possible again. Through compassion, neuroscience, and personalized care, we guide patients toward real recovery and the confidence to move forward with clarity and strength.

The Lasting Impact of Trauma on the Brain and Body

Trauma is more than just a bad memory. It is a deeply physiological experience that leaves a lasting imprint on your brain and body. It doesn’t live solely in the stories you tell; it becomes encoded in your nervous system, altering how you perceive the world, respond to stress, and connect with others. When you experience an event or a series of events that overwhelm your capacity to cope, your brain’s survival mechanisms kick into high gear. While these responses are designed to protect you in the moment, they can become stuck in the “on” position long after the danger has passed.

This chronic state of alert profoundly affects your emotional regulation, making it difficult to feel calm or grounded. It can impact your cognitive function, leading to brain fog and trouble with focus. And it can manifest as physical symptoms, from digestive issues and chronic pain to a weakened immune system. This is why a trauma recovery psychiatry approach must look beyond the psychological story and address the biological changes that have occurred.

Why Understanding Brain Function Is Key to Healing

Understanding the neuroscience of trauma is incredibly empowering. It helps shift the narrative from self-blame (“What’s wrong with me?”) to self-compassion (“This is a normal response to an abnormal situation.”). When you realize that your anxiety, emotional numbness, or reactive patterns are rooted in specific, measurable changes in your brain, it demystifies the healing process.

This knowledge becomes the foundation for targeted, effective treatment. It explains why simply “thinking positively” or “getting over it” is often not enough. Healing involves working with the brain’s natural ability to change—a concept called neuroplasticity—to create new pathways for safety, regulation, and connection. This understanding is particularly crucial when trauma has led to coping mechanisms like substance use.

The Neuroscience of Trauma: What Happens Inside the Brain

To understand trauma’s impact, it’s helpful to look at three key brain regions and how they are affected. Think of them as a security team that gets rewired by a traumatic experience.

1. The Amygdala (The Smoke Detector): This almond-shaped structure is your brain’s fear center. It is constantly scanning for threats. In a traumatized brain, the amygdala becomes overactive and hypersensitive. It starts seeing danger everywhere, even in safe situations. This is why you might feel jumpy, anxious, or constantly on edge. The amygdala trauma response is what keeps you in a state of high alert.
2. The Prefrontal Cortex (The Watchtower): Located behind your forehead, this is your brain’s center for logic, reason, and impulse control. It is supposed to act as the “brakes” on the amygdala’s alarm. After trauma, the connection to the prefrontal cortex can become weakened. It goes “offline” during moments of stress, making it difficult to think clearly, make rational decisions, or calm yourself down.
3. The Hippocampus (The Librarian): This area is responsible for filing memories into a coherent timeline, distinguishing between past and present. Trauma can disrupt the hippocampus, causing memories of the event to remain fragmented and “un-filed.” They don’t feel like they are in the past; they feel like they are happening right now, which is why a sound or a smell can trigger an intense, full-body flashback.

This dysregulation is the core of brain healing after trauma. It’s not about forgetting what happened, but about retraining these brain regions to work together again, so the watchtower can calm the smoke detector and the librarian can file the memories away properly.

How the Nervous System Gets Stuck in Survival Mode

Your autonomic nervous system is what controls your body’s automatic survival responses: fight, flight, or freeze. These are incredibly adaptive in the face of real danger. However, in the aftermath of trauma, the nervous system can get stuck in one of these states.

• Fight/Flight (Hyperarousal): You might feel a constant sense of anxiety, anger, or panic. Your heart may race, your muscles are tense, and you are always on the lookout for danger (hypervigilance).
• Freeze (Hypoarousal): You might feel numb, disconnected, or emotionally flat (dissociation). It can feel like you are watching your life from a distance. This state is also associated with the profound fatigue that many trauma survivors experience.

These aren’t conscious choices; they are ingrained physiological patterns. Healing from trauma involves gently re-teaching the nervous system that the threat is over and that it is safe to return to a state of calm social engagement.

The Ripple Effects: Mood, Sleep, and Cognitive Function

Because trauma dysregulates the most fundamental systems in the brain and body, its effects ripple out into every area of your daily life. It is rarely just about the emotional flashbacks. Many of our patients seeking mental health trauma recovery report a wide range of symptoms that they may not have initially connected to their traumatic experiences.

• Sleep: Trauma sleep problems are extremely common. An overactive nervous system can make it difficult to fall asleep, stay asleep, or experience restful sleep, often leading to nightmares.
• Cognition: Trauma brain fog is a frequent complaint. The chronic stress state can impair memory, concentration, and executive function, making it hard to organize thoughts or complete tasks.
• Mood: The symptoms of PTSD often overlap significantly with those of depression and anxiety, including low mood, anhedonia (loss of pleasure), and persistent worry.
• Physical Health: A chronically activated stress response can lead to digestive issues (like IBS), a weakened immune system (making you more susceptible to illness), and chronic pain conditions.

How Integrative Psychiatry Addresses These Symptoms

An integrative psychiatry approach recognizes that these seemingly separate symptoms are all part of the same interconnected web of trauma. Instead of just prescribing a sleeping pill for insomnia or an antidepressant for low mood, we aim to treat the root cause: the dysregulated nervous system.

At our practice, led by Beata Lewis MD, we use a combination of functional and psychological approaches to rebalance these systems from the ground up. By addressing the biological underpinnings of trauma while simultaneously providing tools for emotional regulation, we offer a path to whole-person healing. This holistic view is central to our comprehensive mental health treatment in Brooklyn.

Functional and Integrative Approaches to Brain Healing

The journey of trauma and brain healing requires a multifaceted approach. A key part of our integrative trauma therapy is using the principles of functional medicine to support the brain’s recovery on a biological level. As a Brooklyn holistic psychiatrist, Dr. Lewis focuses on identifying and correcting the physiological imbalances that can keep the nervous system stuck in survival mode.

This functional trauma treatment often involves:

• Advanced Lab Testing: To look for underlying issues like hormonal imbalances (e.g., dysregulated cortisol), nutrient deficiencies that impact neurotransmitter production, or signs of chronic inflammation that can worsen anxiety and depression.
• Nutritional Psychiatry: Using food as medicine to calm inflammation, balance blood sugar, and provide the brain with the specific nutrients it needs to repair and build resilience.
• Hormone Support: Gently rebalancing the body’s stress hormones to help regulate the nervous system and improve sleep and energy.
• Reducing Inflammation: Identifying and removing triggers of inflammation, which can act like gasoline on the fire of an already activated nervous system.

Therapies That Help the Brain Rewire and Recover

Alongside biological support, targeted therapies are essential for helping the brain process traumatic memories and build new, healthier neural pathways. We utilize a range of evidence-based modalities, including:

• EMDR (Eye Movement Desensitization and Reprocessing): A powerful therapy that helps the brain process and integrate traumatic memories, reducing their emotional charge.
• DBT and CBT: Therapies that provide practical skills for managing intense emotions, challenging negative thought patterns, and navigating relationships.
• Somatic (Body-Based) Work: Techniques that help release trauma stored in the body and teach the nervous system to regulate itself.
• Mindfulness, Breathwork, and Neurofeedback: Supportive practices that strengthen the prefrontal cortex, calm the amygdala, and improve your ability to stay present and grounded.

The BLISS Protocol: A Pathway to Trauma Recovery

Putting all these pieces together can feel overwhelming. That is why we created The BLISS Protocol, our practice’s signature program, to provide a structured, supportive, and comprehensive framework for recovery. The BLISS Protocol for trauma is designed to be a personalized pathway that integrates all the elements of our integrative psychiatry approach.

Within this program, we seamlessly blend advanced lab testing, personalized nutrition, and targeted therapies into one cohesive plan. It removes the guesswork and provides the accountability and expert guidance needed to navigate the complexities of trauma recovery. This integrative psychiatry trauma recovery model ensures that we are not just managing symptoms but are fostering deep, lasting neuroplasticity and healing. 

Building Safety, Resilience, and Self-Regulation

The ultimate goal of our holistic trauma therapy is to help you build a new foundation of safety within your own body. As we repair the nervous system and rebalance your biology, you will begin to notice real-world changes. Your emotional window of tolerance will expand, allowing you to handle stress without becoming overwhelmed. Your confidence will grow as you learn to trust your body and your emotions again. This process of building resilience and self-regulation is the heart of true recovery and a cornerstone of our trauma recovery Brooklyn services, available both in-person and online.

Healing Is Possible: Restoring Balance After Trauma

The path of healing from trauma is rarely a straight line. There will be good days and hard days. But the most important thing to know is that your brain is remarkably capable of recovery. Neuroplasticity is real. You are not broken, and you are not doomed to feel this way forever.

Healing is a partnership, and you don’t have to do it alone. With compassionate guidance, evidence-based tools, and a plan that honors your whole being, you can restore balance to your brain and body. You can move from a life defined by survival to one characterized by connection, meaning, and vitality.

Book your consultation to begin trauma and brain healing with Dr. Beata Lewis in Brooklyn or online.