EMDR for Complex Trauma: Modified Protocols for Dissociation, Developmental Wounds, and the Fragmented Self

Category: Somatic Therapy / EMDR | Level: Jaguar (West) to Hummingbird (North) — Medicine Wheel

---

When the Standard Protocol Is Not Enough

The standard EMDR protocol — eight phases, single-target processing, desensitization to SUD of zero — was designed for single-incident trauma. The car accident. The assault. The natural disaster. A person with a stable pre-trauma personality, a coherent sense of self, adequate affect regulation, and one discrete traumatic memory that disrupted an otherwise functional life.

But what about the person whose entire childhood was the trauma? The person who was never safe, never seen, never held — whose developmental environment was a sustained assault on the capacity to form a coherent self? The person who dissociates when their body is activated, who has parts that do not communicate with one another, who cannot identify a single “worst memory” because there are hundreds, layered and interwoven like scar tissue in connective tissue?

This is complex PTSD (C-PTSD) — a diagnostic entity first described by Judith Herman in 1992 and now included in the ICD-11 (World Health Organization, 2018). Complex trauma produces not just flashbacks and hyperarousal but a constellation of symptoms that the standard PTSD diagnosis does not capture: disturbances in self-organization, chronic affect dysregulation, negative self-concept, and relational difficulties. The person with C-PTSD does not merely have traumatic memories. They have a traumatic identity — a self organized around wound and defense.

Standard EMDR processing in these populations can be destabilizing, retraumatizing, or simply ineffective. The memory network is not a single target but an entire architecture. The affect regulation capacity needed for Phase 4 processing may not exist. The dissociative barriers between parts of the personality may prevent access to key material. The therapeutic relationship itself may be fraught with the transference patterns of early relational trauma.

Over the past three decades, EMDR clinicians have developed a range of modified protocols and adjunctive techniques for complex trauma. This article details the most important of these innovations and their theoretical and empirical foundations.

The Phase-Oriented Approach: Stabilization First

Pierre Janet, the nineteenth-century French psychologist, proposed a three-phase model of trauma treatment that remains the gold standard for complex trauma: (1) stabilization and safety, (2) trauma processing, (3) integration and rehabilitation. Every major authority on complex trauma — Herman (1992), van der Hart, Nijenhuis, and Steele (2006), Courtois and Ford (2009) — endorses this sequential approach.

For EMDR with complex trauma, this means that Phases 1-3 of the standard protocol (History, Preparation, Assessment) may need to be extended for weeks, months, or in severe cases, years before Phase 4 processing can safely begin. The clinician must build the client’s capacity for:

Affect Regulation: The ability to tolerate emotional activation without becoming overwhelmed (hyperarousal) or shutting down (hypoarousal). Ogden, Minton, and Pain (2006) describe the “window of tolerance” — the zone of optimal arousal within which processing can occur. Complex trauma clients typically have a very narrow window: they oscillate between hyperactivation and dissociative shutdown with little middle ground. Stabilization work must widen this window before processing is attempted.

Dual Attention: EMDR processing requires the client to simultaneously hold a traumatic memory in awareness and maintain attention to the present (the therapist’s moving hand, the bilateral taps, the safety of the room). This dual attention is the mechanism by which the memory is processed rather than relived. In dissociative clients, the capacity for dual attention may be compromised — when the traumatic memory is activated, the client loses contact with the present entirely, entering a dissociative state in which processing cannot occur.

Relational Safety: The complex trauma client has been wounded in relationships. Trust is not merely difficult — it is neurobiologically wired as dangerous. The therapeutic relationship must provide a corrective relational experience before it can serve as the container for processing. This requires time, consistency, attunement, and the therapist’s capacity to tolerate the client’s testing, withdrawal, anger, and idealization without retaliating or abandoning.

Shapiro’s AIP Model and Complex Trauma

Shapiro’s Adaptive Information Processing model accommodates complex trauma through the concept of “feeder memories” and “memory networks.” In single-incident trauma, the target is clear: the car accident, the assault. In complex trauma, the presenting symptom (e.g., chronic anxiety in relationships) is connected to a web of memories spanning the developmental period — hundreds of instances of parental unpredictability, criticism, neglect, or abuse.

The AIP model predicts that processing the earliest, most formative memory in a given network (the “touchstone” or “node”) will produce a cascade of generalization effects, resolving later memories in the same network without direct targeting. Clinical experience with complex trauma largely supports this prediction — processing a single early memory (e.g., the first time the client remembers feeling unsafe with a parent) often produces spontaneous resolution of dozens of related memories.

However, complex trauma typically involves multiple, overlapping memory networks, each requiring its own touchstone identification and processing. The treatment plan for complex trauma is therefore a map of networks, not a list of individual targets. Shapiro (2001) describes this as the “three-pronged approach”: past memories that installed the dysfunction, present triggers that activate it, and future templates that establish adaptive responding.

Gonzalez and Mosquera: EMDR for Dissociative Clients

Anabel Gonzalez and Dolores Mosquera, in their 2012 text EMDR and Dissociation: The Progressive Approach, developed one of the most comprehensive frameworks for adapting EMDR to dissociative clients. Their “progressive approach” recognizes that dissociation is not a barrier to EMDR but a phenomenon that EMDR must work with rather than against.

Key principles of their approach:

Assessing Dissociative Structure

Before processing, the clinician maps the client’s dissociative structure: Which parts exist? What are their functions? How do they relate to one another? What material does each part hold? This mapping uses the structural dissociation model of van der Hart, Nijenhuis, and Steele (2006), which describes dissociation as a division of the personality into an “Apparently Normal Part” (ANP) that manages daily life and one or more “Emotional Parts” (EPs) that hold traumatic memories and defensive responses.

In Internal Family Systems language, the ANP functions like a Manager — maintaining the appearance of normal functioning — while the EPs function like Exiles (holding the original pain) and Firefighters (holding the emergency defensive responses). The cross-modal mapping between structural dissociation theory and IFS is clinically useful and theoretically coherent: both models describe a multiplicity of self-states organized around traumatic experience.

Phased Processing

Gonzalez and Mosquera introduce processing gradually:

1. Processing with the ANP first: Begin by processing material that the Apparently Normal Part can tolerate — typically present-day triggers rather than early traumatic memories. This builds confidence in the process and demonstrates that bilateral stimulation is safe.

2. Titrated access to EP material: As the client stabilizes, the clinician facilitates carefully dosed contact between the ANP and the EPs. This might involve the ANP “looking at” the EP from a safe distance (using the conference room technique or similar visualization) and processing the affect that arises in the ANP in response.

3. Direct processing of EP material: Only when the system is stable enough and internal communication is established does the clinician target the traumatic memories held by specific EPs. Even then, processing is titrated — small amounts of material are processed in each session, with careful monitoring of system stability.

Working with Phobic Responses

Gonzalez and Mosquera identify a series of “trauma-related phobias” that must be addressed sequentially:

• Phobia of inner experience (fear of one’s own emotions, sensations, thoughts)
• Phobia of parts (fear of one’s own dissociated self-states)
• Phobia of attachment and attachment loss
• Phobia of traumatic memory
• Phobia of normal life and healthy risk

EMDR can be used to process each of these phobias, beginning with the least threatening and progressing to the most threatening. This sequence respects the structural dissociation model’s hierarchy and prevents the destabilization that occurs when traumatic memory material is accessed before the phobias of inner experience and parts have been resolved.

Jim Knipe: EMDR for Avoidance and Idealization

Jim Knipe’s 2014 text EMDR Toolbox: Theory and Treatment of Complex PTSD and Dissociation addresses a problem that standard EMDR does not: what happens when the client’s protective defenses prevent access to traumatic material?

In complex trauma, the defenses are not incidental obstacles to be overcome. They are survival adaptations that kept the person alive in an environment of chronic threat. Knipe identifies several common defensive patterns and provides EMDR-based interventions for each:

The Loving Eyes Technique

For clients who idealize abusive caregivers (“My father was strict but he loved me”), Knipe developed the “Loving Eyes” technique. The clinician asks the client to visualize looking at their childhood self through the eyes of a wise, compassionate observer. Bilateral stimulation is applied while the client holds this perspective. The technique allows the client to access the truth of their childhood experience without triggering the loyal defense (“My parents did their best”) that protects against the unbearable grief of admitting that one’s caregivers were harmful.

The Back-of-the-Head Scale

Knipe introduced the “back-of-the-head scale” for clients who report a SUD of 0 but whose body language, voice, and autonomic markers suggest significant disturbance. The clinician asks: “If there’s a part of you — maybe in the back of your head — that might feel differently about this memory, what would that part say the SUD is?” This bypasses the dissociative defense and accesses the part that is still holding the disturbance.

Level of Urge to Avoid (LOUA)

For clients whose primary response to traumatic material is avoidance rather than disturbance, Knipe measures the Level of Urge to Avoid (LOUA) alongside the SUD. Processing targets the avoidance itself — the protective response — before targeting the underlying traumatic memory. This sequence respects the protective function of the defense while creating conditions for deeper processing.

The Flash Technique: Processing Without Overwhelm

Philip Manfield and colleagues introduced the Flash Technique (Manfield, Lovett, Engel, & Manfield, 2017) as a method for reducing the disturbance of traumatic memories before standard EMDR processing begins. Flash is particularly valuable for complex trauma clients whose affect regulation capacity is insufficient for standard Phase 4 processing.

The procedure is counterintuitive: the client is asked to focus on a positive, engaging memory or image (not the traumatic material). While attending to this positive focus, the clinician provides sets of bilateral stimulation interrupted by brief (1-2 second) “flashes” of attention to the traumatic memory. The client is instructed to touch the traumatic material only briefly — like touching a hot stove — and return immediately to the positive focus.

The Flash Technique appears to leverage the same working memory mechanism as standard EMDR but with dramatically reduced affective exposure. Clients report significant reductions in SUD after Flash processing, often from 8-10 to 3-4, creating a manageable level of activation for subsequent standard processing.

Wong (2019) conducted a pilot study of the Flash Technique with 10 PTSD patients, finding clinically significant reductions in distress with minimal affective disturbance during processing. Yaşar, Abamor, and Allison (2022) provided further support in a larger sample, demonstrating that Flash reduced SUD ratings significantly within a single session.

The clinical importance of Flash for complex trauma cannot be overstated. The primary barrier to EMDR processing in complex trauma is affective overwhelm — the client’s window of tolerance is too narrow to contain the activation produced by standard processing. Flash provides a way to reduce the charge of traumatic material before opening the processing channel, effectively widening the window of tolerance for subsequent sessions.

Resource Development and Installation (RDI)

Andrew Leeds developed Resource Development and Installation (Leeds, 2009) as a stabilization technique that uses EMDR’s bilateral stimulation to strengthen positive internal resources. RDI is not trauma processing — it is capacity building. It installs the affect regulation, self-efficacy, and relational trust that complex trauma clients need before processing can begin.

The protocol:

1. Identify the needed resource: What capacity does the client lack that prevents processing? Common needs include safety, courage, self-compassion, groundedness, and the ability to ask for help.

2. Access the resource through memory or imagination: The client identifies a time when they experienced this resource (e.g., a moment of feeling genuinely safe) or a figure (real or imagined) who embodies it.

3. Enhance the resource with bilateral stimulation: Short sets of bilateral stimulation (6-12 passes) are applied while the client holds the resource in awareness. Unlike Phase 4 processing, the sets are deliberately short to prevent associative processing from moving to negative material.

4. Install with a cue word: The client associates the resource with a word or gesture that can be used to access it in moments of need.

RDI builds the internal resources that healthy development would have provided. In the Medicine Wheel framework, it is Hummingbird work — the North direction of soul retrieval, recovering capacities that were lost or never developed.

Polyvagal-Informed EMDR

Stephen Porges’ polyvagal theory (2011) provides the neurobiological framework that explains why complex trauma clients respond differently to EMDR than single-trauma clients — and why the modifications described above are necessary.

The polyvagal hierarchy describes three autonomic states:

1. Ventral vagal (social engagement): Safe, connected, present. The myelinated vagus nerve supports facial expression, vocal prosody, and the capacity for calm attention. This is the only state in which adaptive information processing can occur.

2. Sympathetic (fight/flight): Threatened, mobilized, hyperactivated. Heart rate increases, breathing quickens, muscles tense. In this state, the client is reliving rather than processing.

3. Dorsal vagal (freeze/collapse): Overwhelmed, shut down, dissociated. Heart rate drops, breathing becomes shallow, the client “leaves” their body. In this state, processing is impossible.

Complex trauma clients spend most of their time in sympathetic or dorsal vagal states, with limited access to the ventral vagal state. Standard EMDR processing requires sustained ventral vagal activation — the “dual attention” that allows the client to be both here (in the safe therapy room) and there (in the traumatic memory) simultaneously.

The modifications described in this article — extended stabilization, RDI, Flash Technique, titrated processing, dissociative structure mapping — are all strategies for building ventral vagal capacity and ensuring that processing occurs within the ventral vagal state. Every time the client successfully processes even a small amount of material while remaining present and connected, the ventral vagal pathway is strengthened. Over time, the window of tolerance expands, and the client can tolerate increasingly activating material.

Deb Dana’s (2018) clinical application of polyvagal theory provides practical tools for tracking autonomic state in session. The “autonomic ladder” gives clients language for their nervous system states. The “ventral vagal anchor” provides a felt-sense resource for returning to safety when processing moves into activation.

EMDR clinicians working with complex trauma must become skilled readers of the autonomic nervous system. The client’s words may say “I’m fine” while their body says “I am in dorsal vagal shutdown” — flat affect, monotone voice, glazed eyes, shallow breathing. Processing in this state does not produce adaptive resolution. It produces further dissociation.

Integration with Internal Family Systems

The most natural clinical pairing for EMDR in complex trauma work is Internal Family Systems therapy. Richard Schwartz’s model provides the language and framework for the multiplicity of self-states that Gonzalez and Mosquera describe in dissociative terms and that Knipe addresses through his avoidance and idealization protocols.

In practice, the integration works as follows:

1. IFS to identify parts: Before EMDR processing, IFS is used to identify the parts of the system that are involved with the target material. Which part holds the memory? Which parts are afraid of processing? Which parts might sabotage the work?

2. IFS to unblend protectors: If protective parts (Managers or Firefighters) are blocking access to the target memory, IFS techniques are used to negotiate with these parts — to explain the processing, to address their fears, and to obtain permission to proceed. Protectors are not overridden. They are respected as the survival adaptations they are.

3. EMDR to process the memory: Once the parts system is prepared and the Self is in the lead, standard EMDR processing targets the traumatic memory. During processing, parts may emerge spontaneously — an Exile may surface with its original pain, a Firefighter may activate with dissociation or rage. The clinician uses IFS awareness to recognize these shifts and respond appropriately.

4. IFS to integrate after processing: After EMDR desensitization, IFS is used to complete the unburdening — the release of the beliefs, emotions, and body sensations that the Exile has carried. The Exile is invited to let go of its burden and take on new qualities. Protectors are updated — they are informed that the danger they were protecting against has been resolved.

This combined approach — sometimes called “EMDR-IFS” or “parts-informed EMDR” — is increasingly recognized as best practice for complex trauma. It provides the structure and precision of EMDR’s protocol within the relational, parts-sensitive framework of IFS.

Functional Medicine Connections

Complex trauma is not merely a psychological condition. The sustained autonomic dysregulation produced by developmental trauma has profound physiological consequences:

HPA Axis Dysregulation: Chronic stress during development alters the hypothalamic-pituitary-adrenal axis, producing either hyperactivation (elevated cortisol, chronic inflammation) or hypoactivation (cortisol depletion, fatigue, immune suppression). Heim and colleagues (2000) demonstrated that adults with childhood trauma histories show altered cortisol responses to stress that persist decades after the trauma.

Gut-Brain Axis Disruption: Chronic sympathetic activation increases intestinal permeability (“leaky gut”), disrupts the gut microbiome, and contributes to systemic inflammation. Felitti and colleagues’ 1998 Adverse Childhood Experiences (ACE) study demonstrated dose-response relationships between childhood trauma and adult diseases including autoimmune disorders, cardiovascular disease, and metabolic syndrome.

Immune Dysregulation: Danese and McEwen (2012) described the “biological embedding” of stress — the process by which early adversity produces lasting changes in immune function, inflammation, and cellular aging (telomere shortening).

EMDR processing for complex trauma, by resolving the autonomic dysregulation at its source, may produce downstream improvements in these physiological systems. Successful trauma processing shifts the nervous system from chronic sympathetic/dorsal vagal activation to ventral vagal regulation, reducing the sustained stress signaling that drives HPA axis dysfunction, gut permeability, and immune dysregulation.

This is the bridge between somatic therapy and functional medicine: somatic therapies resolve the root autonomic dysregulation; functional medicine addresses the downstream physiological consequences. The most effective treatment for the complex trauma patient integrates both — processing the trauma while simultaneously supporting the body’s recovery through nutrition, gut healing, sleep optimization, and inflammation reduction.

Clinical Safety Considerations

Working with complex trauma using EMDR requires advanced training and clinical judgment. The following safety considerations are non-negotiable:

1. Screen for dissociation before processing: Use the Dissociative Experiences Scale (DES-II; Bernstein & Putnam, 1986) or the Somatoform Dissociation Questionnaire (SDQ-20; Nijenhuis, 1996). Scores above clinical thresholds require modified protocols.

2. Establish stabilization before processing: Ensure the client has adequate affect regulation, a stable life situation, and a strong therapeutic alliance before attempting Phase 4 processing.

3. Monitor autonomic state continuously: Track the client’s autonomic state through observable cues (facial expression, breathing, muscle tension, eye contact, vocal prosody) and intervene when the client leaves the ventral vagal state.

4. Titrate exposure: Use Flash Technique, EMD (eye movement desensitization without reprocessing), or brief processing sets to manage affect intensity. More is not better in complex trauma work.

5. Respect the protective system: Protectors exist for a reason. Overriding defenses through aggressive processing produces destabilization, not healing.

6. Have a closure plan: Every session with a complex trauma client must end with stabilization, regardless of where processing stands. Containment, safe place, and grounding exercises are mandatory.

The work of healing complex trauma is slow, nonlinear, and deeply relational. There are no shortcuts. The clinician’s patience, attunement, and capacity to hold the entirety of the client’s experience — including the parts that push away help — is the foundation upon which all technique rests.

---

References

Bernstein, E. M., & Putnam, F. W. (1986). Development, reliability, and validity of a dissociation scale. Journal of Nervous and Mental Disease, 174(12), 727-735.

Courtois, C. A., & Ford, J. D. (Eds.). (2009). Treating Complex Traumatic Stress Disorders: An Evidence-Based Guide. Guilford Press.

Dana, D. (2018). The Polyvagal Theory in Therapy: Engaging the Rhythm of Regulation. W. W. Norton.

Danese, A., & McEwen, B. S. (2012). Adverse childhood experiences, allostasis, allostatic load, and age-related disease. Physiology & Behavior, 106(1), 29-39.

Felitti, V. J., Anda, R. F., Nordenberg, D., Williamson, D. F., Spitz, A. M., Edwards, V., … & Marks, J. S. (1998). Relationship of childhood abuse and household dysfunction to many of the leading causes of death in adults: The Adverse Childhood Experiences (ACE) Study. American Journal of Preventive Medicine, 14(4), 245-258.

Gonzalez, A., & Mosquera, D. (2012). EMDR and Dissociation: The Progressive Approach. Amazon Imprint.

Heim, C., Newport, D. J., Heit, S., Graham, Y. P., Wilcox, M., Bonsall, R., … & Nemeroff, C. B. (2000). Pituitary-adrenal and autonomic responses to stress in women after sexual and physical abuse in childhood. JAMA, 284(5), 592-597.

Herman, J. L. (1992). Trauma and Recovery: The Aftermath of Violence — From Domestic Abuse to Political Terror. Basic Books.

Knipe, J. (2014). EMDR Toolbox: Theory and Treatment of Complex PTSD and Dissociation. Springer.

Leeds, A. M. (2009). A Guide to the Standard EMDR Therapy Protocols for Clinicians, Supervisors, and Consultants. Springer.

Manfield, P., Lovett, J., Engel, L., & Manfield, D. (2017). Use of the Flash Technique in EMDR therapy: Four case examples. Journal of EMDR Practice and Research, 11(4), 195-205.

Nijenhuis, E. R. S. (1996). Somatoform Dissociation Questionnaire (SDQ-20). [Self-report measure].

Ogden, P., Minton, K., & Pain, C. (2006). Trauma and the Body: A Sensorimotor Approach to Psychotherapy. W. W. Norton.

Porges, S. W. (2011). The Polyvagal Theory: Neurophysiological Foundations of Emotions, Attachment, Communication, and Self-Regulation. W. W. Norton.

Schwartz, R. C. (1995). Internal Family Systems Therapy. Guilford Press.

Shapiro, F. (2001). Eye Movement Desensitization and Reprocessing: Basic Principles, Protocols, and Procedures (2nd ed.). Guilford Press.

van der Hart, O., Nijenhuis, E. R. S., & Steele, K. (2006). The Haunted Self: Structural Dissociation and the Treatment of Chronic Traumatization. W. W. Norton.

Wong, S. L. (2019). Flash technique group protocol for highly dissociative clients in a homeless shelter. Journal of EMDR Practice and Research, 13(2), 116-130.

World Health Organization. (2018). International Classification of Diseases, 11th Revision (ICD-11). WHO.

Yaşar, A. B., Abamor, A. E., & Allison, E. (2022). Application of the Flash Technique for EMDR therapy: A preliminary investigation. Journal of EMDR Practice and Research, 16(1), 30-42.