Selective visual attention requires an efficient coordination between top–down and bottom–up attention control mechanisms. This study investigated the behavioral and neural effects of top–down focused spatial attention on the coding of highly salient distractors and their tendency to capture attention. Combining spatial cueing with an irrelevant distractor paradigm revealed bottom–up based attentional capture only when attention was distributed across the whole search display, including the distractor location. Top–down focusing spatial attention on the target location abolished attentional capture of a salient distractor outside the current attentional focus. Functional data indicated that the missing capture effect was not based on diminished bottom–up salience signals at unattended distractor locations. Irrespectively of whether salient distractors occurred at attended or unattended locations, their presence enhanced BOLD signals at their respective spatial representation in early visual areas as well as in inferior frontal, superior parietal, and medial parietal cortex. Importantly, activity in these regions reflected the presence of a salient distractor rather than attentional capture per se. Moreover, successfully inhibiting attentional capture of a salient distractor at an unattended location further increased neural responses in medial parietal regions known to be involved in controlling spatial attentional shifts. Consequently, data provide evidence that top–down focused spatial attention prevents automatic attentional capture by supporting attentional control processes counteracting a spatial bias toward a salient distractor.