We investigated whether the differences in perceptual awareness for stimuli at the threshold of awareness can arise from different global brain states before stimulus onset indexed by the EEG microstate. We used a metacontrast backward masking paradigm in which subjects had to discriminate between two weak stimuli and obtained measures of accuracy and awareness while their EEG was recorded from 256 channels. Comparing targets that were correctly identified with and without awareness allowed us to contrast differences in awareness while keeping performance constant for identical physical stimuli. Two distinct pre-stimulus scalp potential fields (microstate maps) dissociated correct identification with and without awareness, and their estimated intracranial generators were stronger in primary visual cortex before correct identification without awareness. This difference in activity cannot be explained by differences in alpha power or phase which were less reliably linked with differential pre-stimulus activation of primary visual cortex. Our results shed a new light on the function of pre-stimulus activity in early visual cortex in visual awareness and emphasize the importance of trial-by-trials analysis of the spatial configuration of the scalp potential field identified with multichannel EEG.