What Actually Happens in the Brain During Trauma?

When people hear the word trauma, they often think of events: a car accident, a sudden loss, violence, or abuse. But as trauma specialists, we know that trauma isn’t defined by what happens, it’s defined by how the brain and body respond. Two people can live through the same event, yet one walks away shaken but steady, and the other develops flashbacks, nightmares, or chronic anxiety. The difference lies not in the event itself, but in the nervous system’s capacity to cope.

Understanding what happens in the brain during trauma helps us to move beyond judgment, both of ourselves and others, and toward compassion. It also helps explain why trauma recovery isn’t about “thinking positively” or “getting over it,” but about working gently with a body and brain that learned to protect us at all costs.

In this article, we’ll explore what happens in the brain during trauma, how these changes show up in daily life, and what this means for healing.

The Brain Under Threat

At its core, trauma is the brain’s response to overwhelming threat. When danger is sensed whether physical, emotional, or psychological, the brain automatically activates a survival system designed to protect us.

This system is ancient. Long before we could speak or reason, our nervous systems evolved to detect danger and mobilise us to survive. The main players in this system are:

• The amygdala, the brain’s alarm bell, constantly scanning for threat.

• The hippocampus, which records context, time, and sequence, allowing us to distinguish between “then” and “now.”

• The prefrontal cortex, our rational, reasoning brain that helps us plan, think logically, and regulate emotion.

In a safe state, these areas work together. The amygdala notices something, a loud noise, a raised voice, and quickly alerts the rest of the brain. The prefrontal cortex checks the evidence: “It’s just fireworks.” The hippocampus places the sound in context, “This is New Year’s Eve, not a war zone.” The body might still tense for a moment, but it soon returns to calm. However, when a threat feels overwhelming or inescapable, the system shifts dramatically.

Step 1: The Alarm Sounds - Amygdala in Overdrive

When the brain perceives danger, the amygdala takes command. It does not wait for logic or analysis; it acts instantly, releasing stress hormones like adrenaline and cortisol to prepare the body for survival. The heart races. Breathing quickens. Muscles tense. Blood flow redirects from digestion to the limbs, readying us to fight, flee, or freeze. This is the body’s sympathetic nervous system at work, the accelerator pedal of survival.

In trauma, this system is activated with such intensity that it overwhelms our ability to regulate. The amygdala essentially hijacks the brain, flooding it with fear signals and shutting down nonessential functions like digestion, reproduction, and higher reasoning. In the moment, this is adaptive, it can save your life. But if the alarm system stays on, long after the danger has passed, it can lead to chronic anxiety, hypervigilance, and the feeling that the world is never truly safe.

Step 2: The Context Keeper Shuts Down - Hippocampal Suppression

Under extreme stress, the hippocampus, which usually helps us store memories with a sense of time and place, becomes suppressed. This means that traumatic memories are not encoded like ordinary ones. Instead of being stored as a coherent story, “It happened, it’s over, I survived”, fragments of sensation, sound, and image are stored without sequence or context.

This explains why trauma memories can feel like they are happening right now. A smell, a sound, or a passing face can trigger vivid flashbacks, because the hippocampus did not label the memory as past.

In neuroimaging studies, trauma survivors often show reduced hippocampal volume, reflecting how chronic stress hormones can damage this area over time. The brain literally becomes less able to distinguish between past and present danger.

Step 3: The Thinking Brain Goes Offline - Prefrontal Cortex Inhibition

The prefrontal cortex (PFC) is the part of the brain that helps us reason, regulate emotions, and make decisions. During trauma, it is like the PFC goes dim, because survival takes priority over reflection. In the middle of a threat, stopping to debate options can be fatal. So, the body diverts resources away from higher thinking and into immediate action. This is why trauma survivors often say, “I couldn’t think,” or “I froze.” It is not weakness or failure, it is biology.

In chronic trauma, the PFC can become less active even after the danger ends. This contributes to symptoms like difficulty concentrating, impulsivity, or feeling “foggy.” In therapy, we often see this as the struggle between the rational brain (“I know I’m safe”) and the survival brain (“But it doesn’t feel safe”).

Step 4: The Dissociation Response, When Escape Is not Possible

If neither fight nor flight is possible, as often happens in abuse, captivity, or childhood neglect, the nervous system may switch into freeze or shutdown. This is governed by the dorsal vagal branch of the parasympathetic system, which slows everything down to conserve energy. In this state, people may dissociate feeling numb, detached, or as if they are watching themselves from outside their body.

From a biological standpoint, dissociation is a form of protection, the brain’s way of sparing us from unbearable pain. But when this becomes chronic, it can lead to feelings of emptiness, disconnection, or being “not fully here.” Many trauma survivors describe living as if behind glass, aware but unreachable. Understanding this as a neurobiological response, not a flaw, is a key step toward compassion and healing.

Trauma Changes the Brain (But Not Forever)

One of the most hopeful discoveries in neuroscience over the past few decades is neuroplasticity otherwise known as the brain’s ability to change, adapt, and form new neural connections throughout life. This means that while trauma reshapes the brain, healing can reshape it again.

Trauma leaves a real imprint on neural pathways. Prolonged exposure to stress hormones such as cortisol and adrenaline can lead to structural and functional changes in areas like the amygdala, hippocampus, and prefrontal cortex. These changes help explain many of the symptoms we see in trauma survivors i.e. hyperarousal, emotional dysregulation, memory fragmentation, and difficulty concentrating.

But these neural networks are not fixed. The same brain that learned to survive can also learn to feel safe, connected, and calm. Through therapy, mindful awareness, and relational safety, the nervous system gradually reorganises itself. In other words, when we engage in trauma-informed therapy, mindfulness, somatic practices, or safe relationships, we are not merely learning to manage symptoms, we are literally retraining the brain.

How Neuroplasticity Works

Every experience we have activates neural circuits. When a particular circuit fires repeatedly, it strengthens, forming what we might call a “well-worn path.” In trauma, the brain becomes highly efficient at activating survival pathways: vigilance, fear, withdrawal, or shutdown.

These responses become automatic. Healing involves creating new pathways, ones that associate safety, calm, and connection with particular sensations or contexts. Over time, as these new experiences are repeated and reinforced, the brain begins to favour them. The old trauma-based routes do not disappear entirely, but they become less dominant.

This process is often described by the principle “Neurons that fire together, wire together.” It is why consistency and repetition matter so much in trauma recovery. Each moment of grounding, every time the body feels safety and stays present, contributes to new wiring.

The Role of Safety in Rewiring

The brain cannot rewire while it feels under threat. This is why establishing safety (both internal and external) is the first task of trauma therapy. Safety signals activate the parasympathetic nervous system, particularly the ventral vagal branch, which supports connection, curiosity, and calm. When the body senses safety, the prefrontal cortex can come back online, allowing reflection, integration, and choice.

Healing environments (whether in therapy, community, or relationship) create the conditions for this rewiring to occur. Each time a survivor experiences empathy, attunement, or understanding, their nervous system learns: “It’s possible to feel safe again.”

It is important to note that healing does not mean erasing the trauma or returning the brain to its “pre-trauma” state. Instead, the goal is integration. Integration allows different parts of the brain, (i.e. the emotional, sensory, and rational) to communicate effectively again. When this happens, memories become part of a coherent narrative rather than isolated fragments.

Clients often describe this shift as moving from “It’s happening again” to “It happened, and I survived.” That is the hippocampus and prefrontal cortex working together, bringing the past into the past. However, neural rewiring takes time. The survival brain does not trust easily, and nor should it. Nevertheless, with repeated experiences of regulation, connection, and meaning, the pathways of safety begin to strengthen.

Therapeutic work, body-based practices, and relational repair all offer opportunities for corrective experiences, moments where the brain learns a new outcome is possible. Over time, these moments accumulate into a more stable sense of self, safety, and agency. So, while trauma changes the brain, it does not define it. The same neuroplasticity that once encoded fear and protection can, with care and consistency, encode trust, calm, and connection.

Recalibrating the Amygdala: Teaching the Alarm System to Rest

When someone has lived through trauma, the amygdala (the brain’s internal smoke alarm) becomes highly sensitised. It fires rapidly, even in situations that are objectively safe.

Everyday stimuli such as raised voices, sudden sounds, or conflict can trigger powerful fear responses. Over time, this constant alertness can lead to hypervigilance, panic, and exhaustion. The brain has learned that danger could appear at any moment, so it keeps scanning. The task in healing is not to silence the amygdala, but to help it recalibrate, to relearn what true safety feels like.

Therapeutic and body-based practices help by repeatedly pairing safety with sensations that were once associated with threat.

• Somatic and mindfulness practices teach the body to notice activation without panic. When a client grounds through the senses (e.g. feeling feet on the floor, noticing breath), they send signals of safety up through the vagus nerve.

• Eye Movement Desensitization and Reprocessing (EMDR) and trauma-focused CBT allow clients to recall distressing memories in small, regulated doses. Each time the memory is recalled while the body stays calm, the amygdala “updates” its prediction: “This memory is not dangerous now.”

• Consistent relational safety, otherwise known as being met with empathy rather than threat, is perhaps the most powerful regulator. When the brain experiences repeated, trustworthy connection, the amygdala gradually learns that vigilance is no longer required.

The result is not the absence of fear, but appropriate fear, a system that can distinguish between a true emergency and an echo of the past.

Restoring the Hippocampus: Rebuilding the Brain’s Sense of Time and Story

The hippocampus is like the brain’s internal storyteller. It’s job is to helps us organise experiences in sequence and recognise them as past events. Under chronic stress, cortisol floods this area, impairing its ability to encode coherent memories. That is why trauma memories often return as fragments: sounds, smells, flashes of image without a clear timeline. The hippocampus could not integrate them at the time because survival was the priority.

Rebuilding hippocampal function means helping the brain reconnect the dots between sensory fragments, language, and meaning.

• Narrative work in therapy helps piece together what happened, in a way that feels manageable. As clients put words to sensations and emotions, they engage both the hippocampus and the prefrontal cortex. The memory shifts from being a raw experience to part of a coherent story.

• Mindfulness and grounding support hippocampal recovery by reducing cortisol and re-establishing a sense of now. When clients notice, “I’m safe in this room,” the hippocampus learns to differentiate past from present.

• Lifestyle factors like good sleep, exercise, and social connection have been shown to stimulate neurogenesis (the birth of new neurons) in the hippocampus, restoring its capacity to learn and contextualize.

As this area heals, traumatic memories become integrated rather than intrusive. They can be remembered without reliving. The past finds its rightful place behind us.

Strengthening the Prefrontal Cortex: Reclaiming Regulation and Choice

The prefrontal cortex (PFC) is the seat of our executive functioning. It is the part of the brain that plans, reflects, and inhibits impulses. During trauma, the PFC goes offline because survival does not allow for deliberation. In chronic trauma, the PFC can remain underactive, leading to difficulties such as poor concentration, emotional overwhelm, and impulsive reactions. Healing therefore involves rebuilding the bridge between the thinking brain and the emotional brain.

How Healing Re-engages the PFC

• Mindfulness and focused attention directly stimulate prefrontal activity. When clients practice noticing sensations or breath, they are strengthening neural circuits that allow for pause and reflection.

• Cognitive therapies (like CBT or DBT) help the PFC make sense of emotional experiences, labelling, reframing, and contextualising them. This brings the “top-down” system back online, allowing logic and compassion to coexist with emotion.

• Relational co-regulation also strengthens PFC engagement. When a therapist remains calm and attuned while a client is dysregulated, the client’s nervous system mirrors that steadiness. Over time, the brain learns self-regulation through this modelled safety.

With repeated practice, the prefrontal cortex regains its capacity to observe without judgment, pause before reacting, and make choices rather than automatic defences. Clients begin to notice triggers, take a breath, and respond differently. That moment of pause, however brief, is neuroplasticity in action.

Integrating the Whole Brain

When the amygdala, hippocampus, and prefrontal cortex can communicate effectively again, the person moves from fragmentation to integration.

• The amygdala learns it no longer needs to sound constant alarms.

• The hippocampus reconnects the story of what happened, grounding it in time.

• The prefrontal cortex reclaims its role as wise observer and regulator.

Integration does not mean forgetting the trauma, it means being able to hold the memory without being overtaken by it. It is the difference between “I am terrified” and “A part of me feels terrified, and I can hold that.”

This is the heart of trauma recovery: not erasing the past but integrating it so that the brain and body can return to curiosity, creativity, and connection.

Final Thoughts

Understanding what happens in the brain during trauma is deeply empowering. It reframes symptoms not as signs of failure, but as the body’s intelligent attempt to survive the unbearable.

When clients learn this, they often soften toward themselves: “It makes sense that I react this way.” That self-compassion is not just comforting, it’s curative.

As therapists, we hold the privilege of walking with people as their brains learn safety again. With time, patience, and the right support, the mind that once lived in survival can rediscover curiosity, connection, and calm.

The brain that once braced for threat can learn to trust again, and that, perhaps, is the most profound healing of all.

Photo by Guido Blokker on Unsplash

#trauma #traumatherapy #therapy #psychology #psychologist #traumatheapist #traumapsychologist #ptsd #cptsd #gad #MH #mentalhealth #treatment #recovery #brain #healing #depression #counsellingpsychologist #counselling