Pre-sowing treatment of seeds with cold plasma, a reactive mixture of charged particles, is an emerging, environmentally friendly method, shown to improve water absorption, germination and seedling growth in many crop species. We studied how plasma affects different structural layers in flax seed coats, and focused on the effects on some of the earliest germination events, directly related to imbibition: solute leakage and mucilage extrusion. We characterized the ultrastructure of flax seed coats using scanning electron microscopy (SEM) and observed mucilage extrusion in situ, using environmental SEM. Time-courses of water uptake and solute leakage during germination were recorded, respectively, by weighing the seeds and semi-quantitative metabolite profiling of the exudates using GC-MS, LC-MS and LC-UV. Plasma treatment perforated the cuticle of flax seeds but did not visibly etch the underlying mucilage secretory cell (MSC) walls. Plasma treated seeds took up more water than untreated seeds during imbibition. Mucilage expansion of untreated seeds detached the distal MSC walls from the radial walls and extrusion occurred, relatively slowly, via sparse cracks in the distal cell wall layer. In plasma treated seeds, mucilage extrusion occurred fast, via rupture of distal cell walls of almost every single MSC, and the junctions between distal and radial MSC walls remained intact. Initially, imbibitional solute leakage was higher in plasma treated seeds but the leakage had quasi stopped after one hour of imbibition. In untreated seeds, the leakage continued amply more than two hours after the start of imbibition. Fragments of the lignan macromolecule, stored in parenchymatous cells under the MCS, were released more abundantly in the spermosphere of plasma treated than untreated flax seeds. It is concluded that plasma treatment etches the cuticle of flax seeds and weakens the underlying MSC cell walls, and that such treatment leads to significantly faster recovery of membranes during imbibition, reducing leakage time in germinating seeds.