How Trauma Is Stored in the Body and Impacts the Brain

Trauma isn’t just something that happens in your mind—it’s something your body carries too. It shows up in your nervous system, your muscles, your breath, and your gut. 

It refers to the deep, often invisible wounds caused by overwhelming experiences—moments that shake our sense of safety, control, or predictability. Whether trauma came from a single event or years of chronic stress, it can leave lasting patterns in how we think, feel, and respond to the world around us.

Thanks to modern neuroscience and trauma research, we now understand more about why this happens. When the nervous system doesn’t get a chance to fully process or recover from a threat, the experience may not get stored as a typical memory. Instead, it can live in the body as emotional overwhelm, tension, or sudden reactivity that doesn’t always make sense in the present moment. 

Understanding how trauma is stored in the body and how it shapes the brain can help make sense of symptoms like anxiety, emotional flooding, shutdown, or dissociation. And more importantly, it can point us toward healing. 

What Is Trauma?

Trauma is the body’s response to something overwhelming—an experience (or series of that felt unsafe, threatening, or too much to fully process at the time. It’s not always what happened on the outside—it’s how it registered with you. 

A woman covers her face with her hands, symbolizing the emotional impact of trauma stored in the body.

Trauma can come from:

  • Physical abuse or assault

  • Emotional or psychological abuse

  • Sexual violence

  • Natural disasters or accidents

  • Neglect or abandonment

  • Witnessing violence

  • Religious or spiritual coercion or control

Everyone experiences it differently. What feels traumatic to one person might not have the same effect on someone else. What matters is how your nervous system interpreted the experience and whether you had the support and safety you needed to cope with it.

How Trauma is Stored in the Body

1. The Body Keeps the Score

Coined by trauma expert Dr. Bessel van der Kolk, the phrase "the body keeps the score" speaks to how it leaves a lasting imprint—not just emotionally but physiologically. When we go through something overwhelming, the body’s fight-or-flight system is activated. If the threat isn’t fully resolved, the stress response can stay active and become chronic, and the memory doesn’t get stored like a typical past event.

Instead of being stored as a past event, traumatic memories are stored as sensory fragments—smells, sights, sounds, bodily sensations—that can get triggered unconsciously, without a clear narrative attached.

2. Muscle Memory and Somatic Holding

Traumatic experiences often lead to what’s known as somatic holding patterns—ways the body holds tension and distress from the past. This can show up as, 

  • Tension in the neck, shoulders, or jaw

  • Shallow breathing

  • Chronic pain or gastrointestinal issues

  • Panic-like symptoms without an obvious cause

The body essentially "remembers" what happened even if the conscious mind does not. This is especially evident in people with complex post-traumatic stress disorder (C-PTSD), where the trauma is repetitive, relational, and often invisible to others.

3. The Nervous System and Dysregulation

Trauma can disrupt the autonomic nervous system, which is a part of the body that regulates our automatic functions like heart rate, digestion, and the stress response. When the nervous system is dysregulated, the body can get stuck in cycles of overactivation or collapse. Two common responses are:

  • Hyperarousal: A constant state of alertness, anxiety, or panic

  • Hypoarousal: Numbness, dissociation, fatigue, or shutdown

This dysregulation explains why survivors might fluctuate between states of overwhelm and feeling disconnected. Traditional talk therapy alone may not fully address these patterns, which is why trauma-informed approaches incorporate the body directly. Some examples include: 

  • Somatic Experiencing: Gently releases trapped energy through body awareness

  • EMDR (Eye Movement Desensitization and Reprocessing): Uses bilateral stimulation to help support memory integration

  • Sensorimotor Psychotherapy: Combines body awareness with emotional and  cognitive processing

  • Yoga and movement therapies: Help restore a sense of safety and connection to the body 

These approaches work with the nervous system—not just the story—helping the body release what it’s been holding onto.

How Trauma Impacts the Brain

In addition to affecting the body, trauma also changes how the brain responds to stress, processes memory, and manages emotions. These changes help explain why trauma symptoms can be so persistent even when you logically know you’re safe. 

Here are three key areas of the brain commonly impacted by trauma:

1. The Amygdala—The Alarm System

The amygdala is responsible for detecting danger and triggering the fight-or-flight response. When trauma is present or has occurred, the amygdala becomes hyperactive, constantly scanning for danger—even when none exists. This can lead to:

  • Anxiety or panic attacks

  • Exaggerated startle responses

  • Trouble calming down after conflict

  • Difficulty feeling safe

2. The Hippocampus—The Memory Integrator

The hippocampus helps process and organize memories. In people who’ve experienced trauma:

  • It becomes smaller or less active

  • Memories become fragmented or stored as sensations rather than a clear narrative

  • There may be confusion between past and present (e.g. flashbacks or time distortions)

This is why it can feel like it's happening "right now," even if it occurred years ago.

3. The Prefrontal Cortex—The Rational Brain

The prefrontal cortex is responsible for executive functions like reasoning, impulse control, and decision-making. When the amygdala is overactive, the prefrontal cortex has a harder time doing its job. Trauma reduces its effectiveness, especially during moments of stress or emotional activation. 

As a result:

  • It becomes harder to think clearly under stress

  • Emotions may feel intense or out of control

  • It becomes difficult to differentiate between real and perceived threats

This interaction between the amygdala, hippocampus, and prefrontal cortex helps explain why trauma responses can feel so immediate and overwhelming. The thinking brain may know one thing, but the survival brain takes over.

Why Does It Still Show Up?

Why does it linger long after the event has passed?

The brain stores trauma in survival mode: Unlike normal memories, traumatic experiences are encoded as “this is still happening.”

  • The body maintains physical tension: chronic muscle contractions, shallow breathing, and somatic pain act as constant reminders.

  • Triggers recreate the trauma: Sounds, smells, or sights can unconsciously reactivate the original emotional or physiological response.

  • Protective mechanisms interfere with healing: dissociation, denial, or emotional suppression can delay processing and prolong suffering.

  • Religious trauma adds moral confusion: For those raised in authoritarian or high-control religious environments, trauma may be reinforced by internalized guilt, shame, or fear of eternal punishment.

These lingering effects are why traditional talk therapy may not always be enough. Effective healing often requires therapy that recognizes the body-brain connection and treats trauma as a physiological condition, not just a psychological one.

Healing Through Trauma Therapy

Healing from trauma is not about forgetting or erasing what happened. It’s about processing, integrating, and reclaiming both body and mind. Trauma therapy doesn’t just help people “talk it out.” It supports the body in finding safety again.

Effective therapy recognizes that healing requires attention to both the psychological and physiological aspects. Trauma-informed therapy aims to help survivors:

In a therapy session, one woman holds the hand of another, symbolizing trust and empathy in their conversation.

  • Regulate their nervous system

  • Process traumatic memories in a safe and contained way

  • Challenge negative beliefs shaped by trauma

  • Develop healthy coping mechanisms. 

Modalities like Somatic Experiencing (SE), Eye Movement Desensitization and Reprocessing (EMDR), and Internal Family Systems (IFS) are widely used and have demonstrated effectiveness in supporting trauma recovery.

Conclusion: The Path to Wholeness

Trauma can leave a powerful and often hidden legacy within both the body and the brain, altering our physiology and neural pathways in ways that can make the past feel ever-present. The ongoing effects of trauma are not a character flaw. They’re signs of a nervous system that adapted to survive. By addressing the physical imprint of trauma and its effects on the brain, therapy can help individuals process difficult memories, challenge limiting beliefs, and begin to reclaim their lives. Healing doesn’t mean erasing the past—it means loosening its grip and making space for something new. If you're ready to talk with a therapist, consider scheduling a free 15-minute consultation with Highland Park Holistic Therapy.

Jenny WaltersHighland Park Holistic Therapy