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.