Therapy for my thoughts or my nervous system? An integrated therapy approach explainer

Bottom-up vs Top-down therapy

In graduate school I started taking courses in ‘mental health,’ the phrase alone suggesting health that has to do with the head, thoughts and cognition. In fact, many folks in the counseling profession are licensed as ‘mental health counselors.’ As I began pursuing my interest in trauma-informed therapy, I noticed the trauma world used different language that shifted the focus from the head space to focus on feelings and body sensations. I heard the phrases “top-down therapy” and “bottom-up therapy” and I started asking myself: What do these phrases mean? Is one therapy approach better than the other? Is treating thoughts a separate process from treating emotions? 

I’m not sure I have all the answers, but I love this topic so much I want to get into it. I am confident that in my therapy practice, both top-down and bottom-up therapy approaches have their place in the therapy process, and when used together can create important and effective changes in people’s lives.

Top-down

Top-down approaches have held a foothold in the Western psychology since the time of ancient Greece when philosophers “studied the soul,” a phrase that in Greek combines psyche “soul” and logos “to study” (Psychology4all, n.d.). Their debates introduced the idea of the body and mind being separate from each other, a belief widely adopted in the field of psychology and mental health since. This separation of the mind from the body really flourished during the Age of Enlightenment when reason and rationalism were celebrated and great thinkers began to emphasize the positive impact that rationalism could have on society (History, n.d.).

In the field of psychology, these top-down approaches focus on changing our thoughts and cognitions, which can then lead to positive behavior and prosocial change. They typically entail becoming conscious and aware of what we want to change, putting that awareness or insight into action (practicing new habits, beliefs and patterns), and learning to communicate needs stemming from this insight (Rosenberg, 2015). This can work very well for some folks, however, in my therapy practice I often hear: “I know what I need to change, but I feel stuck” or “I can reframe my thoughts, but I still feel anxious ” or “I see the pattern, but I don’t know how to un-do it.”  And often, these observations are accompanied with feelings of self-judgement or shame.

I have come to understand that the stuck-ness my clients express is because many of the patterns and beliefs we as humans learn are not just thoughts in our mental or cognitive space or behaviors to change, these patterns also live in our nervous system, our bodies and emotional reactions (Badenoch, 2018). This, then, opens the door to bottom-up approaches to therapy.

Bottom-up

Bottom-up approaches are rooted in neurobiology, in the idea that our emotional reactions to the world around us begins in our physiology, that which stems from our body, nervous system, and implicit memory before entering into conscious, cognitive thought (Badenoch, 2018; Olds, 2018; Romero, 2025). While I don’t have the personal lived experience or a citation for it, my sense is that pre/non-Western societies, indigenous and/or Eastern, have more often embraced a greater understanding of this idea, that we are whole, and that the body is an integral part of our experience that informs our thoughts and our conscious experience, that the body and mind are not separate. In the Western psychology world, we began seeing the body/mind divide being bridged in the work of Jung, Adler and the Humanistic movement and slowly a “bio-psycho-social” holistic approach has begun to be normalized (Psychology4all, n.d.). Now, the fields of neuroscience and neurobiology are rapidly growing and expanding to inform the interconnectedness of the human experience, both individually and relationally (Badenoch, 2018; Bridger et al., 2026; Siegel, 2010).

 In therapy, bottom-up approaches focus on gaining awareness of our felt-sense experience and our nervous system reactions, and then working with those reactions in a realistic way. They typically begin with slowing down to notice how something feels in our bodies, what brought that feeling on, and what old stories from our experiences it might feel tied to. Once we notice and validate the reality of how we are feeling, we can honor it by creating safety for that emotion to exist and pass through our body. Once the fire of the emotional reaction eases, it is much easier to access and re-connect to the top-down reasoning abilities we want to put into place.

When the lid is flipped

Expert in interpersonal neurobiology Dr. Dan Siegel describes this process by using what he calls ‘the hand model of the brain’ (Siegel, 2015). In this video, he explains that when our brain stem and limbic areas (the bottom-up areas of the brain which act as an alert to emotional activation) receive information from our nervous system and body sensations that something big is going down, we can actually lose connection with the prefrontal cortex areas of our brain that monitor our reasoning, decision making and moral choices (the top-down area). When we lose contact with that prefrontal cortex (say in a moment of road rage, a panic attack, or a heated argument), Siegel calls that “flipping our lids.”

Once our lid is flipped, our reasoning (top-down) abilities are off-line or hard to reach, and we are purely in reaction mode. Typically, this means our bodies almost automatically find the patterns of fight, flight, freeze, fawn, submit, etc that we began to use in childhood to get through difficulties in life which became stored in our implicit memory and nervous system (Olds, 2018). This might look like screaming in an angry outburst or freezing in fear, people pleasing even when we normally wouldn’t or shutting down to avoid something that feels frustrating or insurmountable.

It is important to note that the human body was honed through evolution to flip our lids to deal with extreme danger. If a lion is attacking, we don’t need to think through our survival options before reacting, we need to immediately react. Once our systems register incoming information as 'lion attack’ an immediate reaction bypasses thinking (top down), and moves us to action (bottom up): to fight, flee or play dead…. whatever is needed to survive that moment (Levine, 1997).

However, society has evolved and changed. While late-stage capitalism does indeed carry real dangers, especially for folks marginalized and othered by those in power who hold the most resources, these same survival responses may not always be as helpful for today’s dangers as ancient dangers. Now, the survival triggers for our nervous systems might come from information overload in a digitally saturated world, feeling alone in a hyper-individualized society, figuring out how our life path can create access to money to feed our families, and burnout. This could be a whole other topic to write about, as there is nuance here for sure. This paragraph is about honoring the complexity of being human. That we as modern humans have evolved with ancient nervous systems designed to ‘flip our lids’ – for survival. This dismantles judgement around reacting before thinking. It will happen to all of us.

Of course, lids don’t stay flipped. The top-down abilities to reason do come back to meet the bottom-up information our bodies have acted on. Typically, once the emotional surge of information (threat-detection) passes, the connection to our prefrontal cortex resumes. This might include realizing we can’t control another driver’s actions on the road, that the source of the panic attack was not life-threatening or is actually something we can process more slowly, or that the other person in our argument had a pretty good point.

In the context of relationships, Siegel (2015) also mentions the importance of coming back to repair with loved ones when we flip our lids in such a way that we unintentionally harm people we care about.

Relational side quest: Balancing accountability for flipping our lids without shame and judgment

Sometimes when our lids come back online, the reconnection is accompanied by guilt or shame regarding the actions we took while our lid was flipped. Let’s do a quick recap of guilt vs shame and how they tie in with top-down and bottom-up therapy approaches.

In the case of guilt (I did something harmful): guilt leads us to make positive future life choices, like making amends. It can’t be stressed enough that accountability to our loved ones, and to the world around us is paramount. It is so important to take accountability and make a repair with other people or pets that we unintentionally harmed while our lid was flipped. Making amends, apologizing, showing we care, and accepting that mistakes are made sometimes is actually part of what brings us closer and builds a sense of belonging and connection (Tronick & Gold, 2020).

With guilt, learning top-down approaches in therapy can bring about change. We can lean into creating cognitive awareness that we flipped our lid, exercise curiosity, understand the triggers that led us to that point, learn and role-play how to communicate more effectively (Rosenberg, 2015), and build better relationship habits for the future. These are all ways top-down therapies can help move guilt into something positive.

Regarding shame (I am bad), feeling shame does not motivate more positive behavior (Schwartz & Sweezy, n.d.). It typically inhibits us from action or comes out as aggression. Shame is a learned emotion that is stored in the body and nervous system. If left untended, shame can become part of the cycle mentioned earlier: “I know what I need to change, but I feel stuck” or “I see the pattern, but I don’t know how to un-do it.”  Often, shame does not allow us the room to accept that we are human, that our lids will flip, and inhibits us from realizing we might be able to work with the information flow our nervous systems are experiencing in any given moment.

The key to working with shame is to validate implicit memories stored in the nervous system of early key moments in life that got stored as sensations of “I must have done something wrong, I am bad.”  Working to witness and release the shameful messages we took on is part of the therapy process, and in my experience, this is where bottom-up therapy approaches are most helpful. This might look like recognizing how shame feels in our bodies, allowing it to be witnessed with a safe other when it shows up, and parts work. For example, building awareness and a relationship with our own young parts that began to take on messages like ‘I am bad’ as a way to make sense of what was happening around them (Schwartz, 2021; Schwartz & Sweezy, 2020).

Whether working with guilt, shame or both, it is important to accept that our thinking brains will sometimes go off line in favor of pure emotion based reactions. Healing occurs when we recognize bottom-up impulses as signals and information, validate them as normal emotional activations, tend to them as we ride the wave of the emotion, and use the information to create meaning that informs empowered future top-down cortical processes.

What do top-down and bottom-up approaches look like in the therapy room?

A top-down approach will likely include a lot of verbal processing. Acronyms like CBT, CPT, DBT, ACT all refer to cognitive-leading approaches (respectively: Cognitive Behavior Therapy, Cognitive Processing Therapy, Dialectical Behavior Therapy, and Acceptance and Commitment Therapy). Cognitive and behavior-based approaches often reality-check the stories that we automatically tell ourselves (“Is this story I am telling myself actually true?”), untangle grey areas from what we assume is black and white, re-route negative thought patterns, and create action plans for the future to enact the changes we want to make. Top-down therapy will likely include curiosity-based questioning, referred to as Socratic dialogue, in which a therapist asks questions that help reveal how and why a client believes things, and invites space to reflect on how helpful or unhelpful these thoughts are to the client’s functioning (Uniformed University Services, n. d.). This process of thoughtful, compassionate and curiosity-based questioning can help create deep insight as well as perspective and meaning making for clients.

Bottom-up approaches will show up a little differently in the therapy process. They might include therapist prompts to slow down, to notice body sensations, emotions or images that come up with the topic at hand. In my work with clients, I often make time in one of our first sessions to educate clients on the nervous system, how we are constantly taking in information consciously and unconsciously, and interpreting safety and danger which informs the state of our current experience (Walker, n. d.). Bottom-up approaches use the body, metaphor or art, imagery, or symbolism to tap into right brain ways of making sense of life experiences. EMDR therapy, Art Therapy, Somatic Experiencing, Jungian work and Gestalt therapy also work from a bottom-up approach.

For me, parts work is a key bottom-up approach. Using an internal family systems (IFS) lens, we might get to know protective parts that have learned to strive to act perfectly, to criticize or avoid, or that carry hurt. We invite these parts to help us understand when they started doing their work to help us survive, and what might have prompted their decision (Schwartz, 2020). How might a part of us be shaping the interpretation of safety and danger signals from the nervous system? This helps create clarity about when and how patterns of personal beliefs start, and in what context. The power of bottom-up parts work in IFS lies in opening to compassion, building a relationship to Self, witnessing how hard parts work to protect us, and creating awareness around the conditions that wounds became burdens, which allows the burden to be released. To my parts that thrive in a top-down ‘figure it out’ culture, it can feel confusing to try to understand the felt-sense of the bottom-up learning. But there is power in being a compassionate presence to ourselves, and to opening that space in the therapy relationship. The goal in bottom-up approaches is to bring presence to what is going on in the system.

The combined approach sweet spot

For me, a combined approach is the sweet spot. Typically, both approaches show up several times in the span of one therapy session. Combining the top-down approach of encouraging insight and motivation for change with the felt-sense depth of bottom-up approaches is what leads to lasting change.

As a therapist, this requires staying attuned to:

• Which approach the client leads with. Some clients lean more toward intellectualizing while some feel things so deeply it is hard to get out.

• How to invite space for the alternate approach when needed. For instance, phase 4 of EMDR therapy can be excellent for cognitive leaning clients to help connect to the felt-sense experience. And for the deep feelers, honoring context and perspective can be helpful as they learn and practice coping skills to ride the waves of emotion.

• Tracking my own therapist parts. When are my own top-down intellectualizer parts present, trying to figure things out, and when are my empathic feeling-with parts  present? Recognizing them can help me make sure they don’t impede the therapy process, or when I need to speak for them to make a repair.

• Normalizing the importance of BOTH the ‘knowing’ and the ‘feeling.’

  
  

What seems small might loom large – an example

Combining top-down and bottom-up approaches broadens the definition of trauma, and creates insight around things from our past that don't seem to count as traumatic. For example, I often encounter clients that discount childhood memories that “seem small" – like being told not to cry as a child, which is often linked to an assigned gender role “be a man, don’t cry.” That "small" message starts to shape a nervous system toward a pattern of responses - maybe a clenching sensation, stifling emotions, stuffing them down, hoping they disappear or pretending they don't matter. That "small" message might start creating identity belief patterns “I’m not allowed to have feelings;” relational belief patterns “I will not be accepted if I express emotion;” behaviors that redirect to an emotion perceived as more acceptable – “I’m not supposed to cry, so I’ll yell, that’s what real men do;” fear of emotion itself, or of being able to ‘handle’ certain emotions. Once that "small" message (pattern of neural firings) is created, it is deepened each time life experiences “confirm” it.

Bottom-up approaches recognize that under unhelpful behaviors (yelling instead of crying) there may be desperation or extreme states of emotion that have never known they needed care and attention. Once validated with concious awareness as something significant, not "small" at all, then we can invite top-down approaches in to help make desired changes in every day life (communicating openly and honestly, or adopting the empowering belief that an emotion is not a sign of weakness).

What an integrated approach considers

An integrated approach top-down and bottom-up approach considers the following:

• Questions: “What happened to you, and how did you survive?” instead of “What is wrong with you?”

• Affirms: “Your past behavior makes sense, given what has happened to you. Now, lets work to update and find alternate behaviors if needed.”

• Asks: “What is the root cause, even if it feels small, so we can address it and resolve?”

• Validates: “The parts that have caused extreme behaviors have been working really hard for a long time.”

When used together, both top-down and bottom-up approaches ideally begin with a non-judgmental stance, accepting the person within the context of their experiences. The client is the expert on themselves, and the therapist is there to help facilitate the process by inviting compassion and heart-centered guiderails to remind client parts carrying pain and shame they are not alone. Together, client and therapist become curious about a client’s way of being in relationship, both with Self and others, to better understand the function of a pattern and address it with an updated change or with care.

References:

Badenoch, B. (2018). The heart of trauma: Healing the embodied brain in the context of relationships. W.W. Norton.

Bertelli, C. (2026, June). Why positive thinking doesn’t fix anxiety (and what actually does). https://www.cedricbertelli.com/blog/why-positive-thinking-doesnt-fix-anxiety

Brewer, J. A. & Giommi, F. (2025). Psychotherapy as investigation: cultivating curiosity and insight in the therapeutic process. Frontiers in Psychology, 16:1603719. https://doi.org/10.3389/fpsyg.2025.1603719  

Falkenstein, B., Savage, J., & Boston, C. (2026, Jan 23). Keeping up with EMDR, the brain, and neurobiology: From brain parts to brain networks. EMDRIA. https://www.emdria.org/blog/keeping-up-with-emdr-the-brain-and-neurobiology-from-brain-parts-to-brain-networks/

Fee, J. (2024). Integrating EMDR therapy with cognitive behavioral approaches. EMDRIA Focal Point Blog. https://www.emdria.org/blog/integrating-emdr-therapy-with-cognitive-behavioral-therapy-cbt/

History.com. (n.d.). Enlightenment. https://www.history.com/articles/enlightenment

Kotler, S., Mannino, M., Fox, G., & Friston, K. (2026). The body does not keep the score: Trauma, predictive coding, and the restoration of metastability. Frontiers in Systems Neuroscience, 20, 1812957. https://doi.org/10.3389/fnsys.2026.1812957  

Lanius, R. A., Harricharan, S., Kearney, B. E., & Pandev-Girard, B. (2025). Sensory pathways to healing from trauma: Harnessing the brain's capacity for change. Guilford Press.  

Levine, P. (1997). Waking the tiger. North Atlantic Books

Olds, T. (2018, Dec 18). Memory reconsolidation: How to rewire our brain. YouTube. https://www.youtube.com/watch?v=PWfpLtgxDi4

Padesky, C. & Mooney, K. A. (2012). Strengths-based cognitive-behavioral therapy: A four-step model to build resilience. Clinical Psychology & Psychotherapy, 19(4), 283-290. https://doi.org/10.1002/cpp.1795 

Romero, B. (2025). The bottom-up vs. top-down approach in therapy: Understanding the path to healing. https://www.lotusmindflow.com/mental-health-trauma-informed-blog/the-bottom-up-vs-top-down-approach-in-therapy-understanding-the-path-to-healing

Rosenberg, M. (2015). Nonviolent communication. Puddledancer Press.

Schneider, S. M., & Morris, E. K. (1987). A history of the term radical behaviorism: From Watson to Skinner. The Behavior Analyst, 10, 27-39. Open

access: https://doi.org/10.1007/BF03392404

Schwartz, R. C. (2021). No bad parts: Healing trauma and restoring wholeness with the internal family systems model. Sounds True.

Schwartz, R. C & Sweezy, M). (n.d.). Applying internal family systems to complex clinical issues: Treating Shame from an IFS Perspective [Online course]. National Institute for the Clinical Application of Behavioral Medicine (NICABM). https://www.nicabm.com/

Schwartz, R. C. & Sweezy, M. (2020). Internal family systems therapy (2^nd ed). Guilford Press.

Shapiro, F. (2018). Eye movement desensitization and reprocessing (EMDR) therapy: Basic principles, protocols, and procedures (3rd ed). Guilford Press.  

Siegel, D. J. (2020). The developing mind: How relationships and the brain interact to shape who we are. The Guilford Press

Siegel, D. (2011). Mindsight. Bantam Books

Siegel, D. (2015, July). Daniel Siegel hand model. YouTube. https://www.youtube.com/watch?v=qFTljLo1bK8

Tronick, E. & Gold, C. M. (2020). The power of discord: Why the ups and downs of relationships are the secret to building intimacy, resilience, and trust. Scribe Publications.

Uniformed University Services. (n.d.) Socratic dialogue. https://deploymentpsych.org/content/socratic-dialogue

Psychology4all. (n.d.) A short history of Western Psychology. https://www.psychology4all.com/index.php/history-of-psychology?view=article&id=49

Walker, R. J. (n.d.). Polyvagal theory. Southwest Trauma Training. https://www.swtraumatraining.com/polyvagal-theory