Emotions are not confined to short momentary states but carry on over time, facilitating the perception and interpretation of the environment in mood-congruent ways. Yet, the (neural) mechanism linking affective stimulation at a certain time-point to such altered, mood-congruent processing of stimuli presented at a subsequent time-point remains unknown. Recent research suggests that such a link could be explained by transient effects of affective stimulation on the organization of intrinsic macro-scale neural networks. It remains, however, unclear whether these changes in network organization are influencing subsequent perception in a mood-congruent way. Addressing this gap the current study investigated whether changes in network organization, measured in terms of network efficiency, mediate the relation between mood-induction and mood-congruent processing as measured by reaction-times during an emotional Stroop task. The results demonstrated that negative mood-induction increased the efficiency of the Salience Network and decreased the efficiency of the Central Executive Network. This modulation of network efficiency fully mediated the effects of mood-induction on reaction-times to negative words. These findings indicate that transient shifts in the organization of macro-scale neural networks are an essential part of the emotional response and can help to explain how affect shapes our interaction with the environment.