The goal of the present study was to investigate the initial phases of novel grammar learning on a neural level, concentrating on mechanisms responsible for individual variability between learners. Two groups of participants, one with high and one with average language analytical abilities, performed an Artificial Grammar Learning (AGL) task consisting of learning and test phases. During the task, EEG signals from 32 cap-mounted electrodes were recorded and epochs corresponding to the learning phases were analysed. We investigated spectral power modulations over time, and functional connectivity patterns by means of a bivariate, frequency-specific index of phase synchronization termed Phase Locking Value (PLV). Behavioural data showed learning effects in both groups, with a steeper learning curve and higher ultimate attainment for the highly skilled learners. Moreover, we established that cortical connectivity patterns and profiles of spectral power modulations over time differentiated L2 learners with various levels of language analytical abilities. Over the course of the task, the learning process seemed to be driven by whole-brain functional connectivity between neuronal assemblies achieved by means of communication in the beta band frequency. On a shorter time-scale, increasing proficiency on the AGL task appeared to be supported by stronger local synchronisation within the right hemisphere regions. Finally, we observed that the highly skilled learners might have exerted less mental effort, or reduced attention for the task at hand once the learning was achieved, as evidenced by the higher alpha band power.