Introduction An increasing number of studies are using magnetoencephalography (MEG) to study dementia. Here we define a common methodological framework for MEG resting-state acquisition and analysis to facilitate the pooling of data from different sites. Methods Two groups of patients with mild cognitive impairment (MCI, n = 84) and healthy controls (n = 84) were combined from three sites, and site and group differences inspected in terms of power spectra and functional connectivity. Classification accuracy for MCI versus controls was compared across three different types of MEG analyses, and compared with classification based on structural MRI. Results The spectral analyses confirmed frequency-specific differences in patients with MCI, both in power and connectivity patterns, with highest classification accuracy from connectivity. Critically, site acquisition differences did not dominate the results. Discussion This work provides detailed protocols and analyses that are sensitive to cognitive impairment, and that will enable standardised data sharing to facilitate large-scale collaborative projects.