Developmental stuttering is a fluency disorder with anomalies in the neural speech motor system. Fluent speech requires multifunctional network formations. Currently, it is unclear which functional domain is targeted by speech fluency interventions. Here, we tested the impact of fluency-shaping on resting-state fMRI connectivity of the speech planning, articulatory convergence, sensorimotor integration, and inhibitory control network. Furthermore, we examined white matter metrics of major speech tracts. Improved fluency was accompanied by an increased synchronization within the sensorimotor integration network. Specifically, two connections were strengthened, left laryngeal motor cortex and right superior temporal gyrus showed increased connectivity with the left inferior frontal gyrus. The integration of the command-to-execution and auditory-motor pathway was strengthened. Since we investigated task-free brain activity, we assume that our findings are not biased to network activity involved in compensation. No alterations were found within white matter microstructure. But, brain-behavior relationships changed. We found a heightened negative correlation between stuttering severity and fractional anisotropy in the superior longitudinal fasciculus, and a heightened positive correlation between the psycho-social impact of stuttering and fractional anisotropy in the right frontal aslant tract. Taken together, structural and functional connectivity of the sensorimotor integration and inhibitory control network shape speech motor learning.