Part 2: The Neurobiology of Safety — How the Vagus Nerve Shapes Trauma and Healing
By Kelley Winters, EMDR Therapist | Denver Wellness Counseling
Introduction: Safety Is a Biological Experience
When clients begin trauma therapy, they often say, "I know I'm safe — but my body doesn't believe it." That statement captures the heart of the Polyvagal perspective.
Our brains and bodies don't heal simply because we think we should; they heal when our nervous system feels safe enough to let its guard down.
At Denver Wellness Counseling, our therapists help clients increase their awareness of how and why their bodies react based on their intrinsic Polyvagal System. In addition, we encourage the use of body based tools like Vagus Nerve Stimulation to help our clients' grow their ability to create a felt sense of safety when they are safe. Understanding and creating the "neurobiology of safety" is an important beginning step of EMDR therapy for Denver Wellness Counseling clients.
Neuroception: The Body's Inner Security System
Neuroception is the body's automatic process of scanning for safety or threat. Unlike perception, which is conscious, neuroception happens below awareness.
When neuroception detects safety, the ventral vagal system switches on. You can connect, feel present, and trust your environment.
When it senses danger, your sympathetic system prepares you to fight or flee.
If danger feels inescapable, the dorsal vagal system triggers a freeze or shutdown to conserve energy.
For trauma survivors, this detection system becomes overly sensitive. Everyday stressors — a tone of voice, a slammed door, even silence — can register as threat signals. That's why trauma therapy starts with retraining neuroception to identify genuine safety.
How Trauma Alters the Neurobiology of Safety
Chronic or overwhelming trauma rewires how the nervous system interprets signals.
The amygdala (alarm system) becomes hyperactive.
The hippocampus (memory integration) struggles to sort past from present.
The prefrontal cortex (logic and reasoning) goes offline when danger feels near.
This is why someone can know they are safe yet still feel panicked. The nervous system hasn't received enough consistent messages of safety to update its response.
Trauma therapy — and particularly EMDR Trauma Therapy—can reduce the intensity of the brain's alarm system (desensitization) and can provide opportunity for the brain regions to reconnect in an updated manner (reprocessing). Through the process of EMDR, the brain's sensitivity to triggers and traumatic memories is reduced and the brain has more space and flexibility to identify true safety or danger in the present moment.
The Vagus Nerve and Vagal Tone: The Brain-Body Connection
The vagus nerve functions like a switch board connecting your body to your brain's perception and neuroception of safety or danger around you. When the brain senses danger, the vagus nerve sends signals to your body to prepare for danger. This might include increased heartbeat and breathing rate, a surge of energy in the body, muscle tension, and an overall sense of alert that is experienced as a form of anxiety. When the brain senses safety, the vagus nerve sends signals to the body that allow for relaxation, rest, digestion, immune function, and connection with others.
The vagus nerve connection is a two way switch board. When relaxation and low tension are present in the body, the brain receives messages of safety that allow for connection with others, expanded thinking, and creative problem solving. Conversely, when increased tension, elevated heart rate, or shortness of breath are present in the body, the brain receives messages of danger prompting alert, hypervigilant, and protective thought patterns.
The ability of your nervous system and body to move between a sense of safety and danger is known as vagal tone. High vagal tone means you can slow down after stress, recover quickly, and re-engage socially. Low vagal tone means you stay revved up or shut down long after the danger has passed.
You can actually strengthen and increase vagal tone through practice — just like exercising a muscle. Practicing vagus nerve stimulation techniques such as breathing exercises, gentle humming, and co-regulation with supportive others.
Try This: 3-Minute Vagus Reset
Whenever you feel tense or disconnected, try this mini-practice:
Orient: Slowly look around. Name 3 things you see and 2 things you hear.
Soften: Drop your shoulders, unclench your jaw.
Breathe: Inhale through your nose 4 counts → exhale through your mouth 6–8 counts.
Hum or sigh gently: Vibration activates the vagus nerve.
Notice: Do you feel a little more present or connected?
With repetition, your nervous system learns: I can influence my state.
Co-Regulation: How Connection Heals the Nervous System
Humans are wired for connection. From infancy, we regulate through others: a caregiver's voice, a friend's calm tone, a therapist's grounded presence.
In trauma therapy, co-regulation often looks like:
Slowing your breathing together with your therapist
Noticing when eye contact feels safe or activating
Feeling your heartbeat steady as you sense connection
This isn't small talk — it's nervous-system work. Co-regulation teaches your body that connection is safe again, restoring ventral vagal pathways that trauma disrupted.
The Window of Tolerance
Dr. Dan Siegel coined the phrase "window of tolerance" to describe the range in which we can think, feel, and function effectively.
Inside the window: regulated, connected, able to reflect.
Above the window: hyper-aroused — anxiety, panic, rage.
Below the window: hypo-aroused — numbness, disconnection, exhaustion.
Polyvagal awareness helps you notice where you are on this map and use tools to return to your window. Expanding this window is a key goal of EMDR preparation.
Why Vagal Tone Matters in EMDR Therapy
EMDR uses bilateral stimulation — eye movements, taps, or tones — to help the brain reprocess traumatic memories. When your vagal tone is high and your window of tolerance is wide, EMDR can do its job smoothly.
But if your nervous system is still dysregulated, reprocessing may feel too intense. That's why Polyvagal-informed preparation ensures:
You can recognize early signs of dysregulation.
You have tools to return to safety between sets.
Your body trusts that it can come back to calm after activation.
This combination of body awareness and EMDR makes therapy both safer and more effective.
How a Denver Wellness Counseling Therapist Strengthens Safety Before Trauma Work
At Denver Wellness Counseling, we weave Polyvagal-based interventions into early EMDR phases:
Practicing long-exhale breathing to cue the vagus nerve.
Using orientation exercises ("Look around the room; what feels safe?").
Adding bilateral tapping while focusing on calming imagery.
Building co-regulation with the therapist before targeting past trauma.
These steps create a foundation of trust — both within yourself and within the therapeutic relationship.
Healing is Possible
Over time, Polyvagal-informed EMDR therapy helps your nervous system learn new patterns:
Safety feels familiar, not foreign.
Connection feels regulating, not risky.
Stress recovery becomes faster and easier.
Healing is less about never feeling triggered and more about trusting your body's ability to return to safety.
The Takeaway
Building a flexible nervous system that can signal your body to move between a felt sense of danger and safety is an important part of your trauma healing. At Denver Wellness Counseling we work with you to identify and establish your neurobiological pathways of safety. When your body can feel safe, your mind can finally let go of old fear loops and EMDR is most effective.
If you're exploring EMDR therapy in Denver, and want to prepare your nervous system for the journey, Polyvagal-informed EMDR therapy can make all the difference.
