Dynamic systems theory suggests that instability can be a key element in the promotion of human change processes. Several studies have confirmed an association between unstable patterns and successful psychotherapeutic outcome. Somewhat similarly, the assimilation model of psychotherapeutic change argues that clinical change occurs through the integration of problematic experiences that initially threaten the stability of the self. This study examined how instability in assimilation levels was related to assimilation progress and change in symptom intensity, within and across sessions, in a good-outcome case of Emotion Focused Therapy. We used the assimilation of problematic experiences scales (APES) to measure assimilation and the outcome-questionnaire (OQ-10) to measure clinical symptom intensity. To assess assimilation instability, we used a fluctuation measure that calculated the amplitude and the frequency of changes in assimilation levels. To analyze the structural relationships between variables we used a dynamic factor model. The results showed that APES level and APES fluctuation tended to increase across treatment, while OQ-10 scores tended to decrease. However, contrary to expectations, the dynamic factor model showed no significant associations between APES fluctuation and OQ-10 scores either within sessions or between adjacent sessions.