Mindfulness-based meditation practices involve various attentional skills, including the ability to sustain and focus ones attention. During a simple mindful breathing practice, sustained attention is required to maintain focus on the breath while cognitive control is required to detect mind wandering. We thus hypothesized that regular, brief mindfulness training would result in improvements in the self-regulation of attention and foster changes in neuronal activity related to attentional control. A longitudinal randomized control group EEG study was conducted. At baseline (T1), 40 meditation naïve participants were randomized into a wait list group and a meditation group, who received three hours mindfulness meditation training. Twenty-eight participants remained in the final analysis. At T1, after eight weeks (T2) and after 16 weeks (T3), all participants performed a computerized Stroop task (a measure of attentional control) while the 64-channel EEG was recorded. Between T1 and T3 the meditators were requested to meditate daily for 10 min. Event-related potential (ERP) analysis highlighted two between group effects that developed over the course of the 16-week mindfulness training. An early effect at left and right posterior sites 160–240 ms post-stimulus indicated that meditation practice improved the focusing of attentional resources. A second effect at central posterior sites 310–380 ms post-stimulus reflects that meditation practice reduced the recruitment of resources during object recognition processes, especially for incongruent stimuli. Scalp topographies and source analyses (Variable Resolution Electromagnetic Tomography, VARETA) indicate relevant changes in neural sources, pertaining to left medial and lateral occipitotemporal areas for the early effect and right lateral occipitotemporal and inferior temporal areas for the later effect. The results suggest that mindfulness meditation may alter the efficiency of allocating cognitive resources, leading to improved self-regulation of attention.