Activation of transversus abdominis and fear avoidance beliefs have both been related to low back pain (LBP). This exploratory study aims to investigate associations between fear avoidance beliefs at baseline and deep abdominal muscle activation after an 8-week period of supervised exercises for chronic LBP. A cohort of patients with chronic non-specific LBP (N = 108) enrolled in a clinical trial was studied longitudinally. Fear avoidance beliefs for physical activity and work were measured before intervention. Activation in transversus abdominis and obliquus internus abdominis during abdominal drawing-in manoeuvre and rapid arm flexion was measured by ultrasound before and after intervention. Associations between baseline fear avoidance beliefs and deep abdominal muscle activation after exercises were analysed with multiple linear regression methods. High fear avoidance beliefs for physical activity (≥16 on the subscale) were negatively associated with transversus abdominis slide after the intervention period, β = -4.92 (-8.40 to -1.45). There were no associations between fear avoidance beliefs for physical activity and abdominal muscle onset, transversus abdominis or obliquus internus contraction ratio. Fear avoidance beliefs for work were not associated with any of the muscle activation parameters. This study suggests that there is some negative association between fear avoidance beliefs for physical activity before intervention and transversus abdominis recruitment measured by lateral slide after intervention. No other significant associations between fear avoidance beliefs and abdominal muscle activation were found. We cannot exclude random findings, meaning that the results should be considered hypothesis generating for further investigations.