Method for holding substrates on a flatbed printing system. After positioning the substrates on the substrate support surface, a leak air area not covered by the substrates is covered by positioning a flexible cover device at least over the leak air area, and preferably over the substrates as well. Thereby, air flow through the through-holes is prevented. An under-pressure is then applied to the through-holes, sucking the substrates against the substrate support surface. The flexible cover device is then withdrawn to expose the substrate for printing while the under-pressure is maintained. It was found that despite the additional amount of air passing through the through-holes uncovered by the withdrawal of the flexible cover device, the under-pressure surprisingly remained sufficient to properly hold the substrates for printing. An additional advantage is that the cover device may be applied easily and rapidly over the leak air area and substrates at once.