An apparatus (100) for manufacturing capsules (10) under vacuum for preparing beverages is described, comprising: a plurality of support elements (105) and a driving system (120) adapted to move said support elements (105) and stop them in a plurality of operative stations, wherein each support element (105) comprises a row of housing seats (115), wherein the operative stations comprise at least: a loading station (145) for inserting into the housing seats (115) a glass-shaped body (15), a filling station (150) for filling glass-shaped bodies (15) with a food substance adapted to produce a beverage, a covering station (155) for applying and fixing on the glass/shaped bodies (15) a closing film (45), and a sealing station (160) for placing under vacuum the inner volume of the glass-shaped bodies (15) and for sealing the closing film (45) and wherein said sealing station (160) comprises: a plurality of bell-shaped members (280), each of which is adapted to overlay to one respective housing seat (115) and has mouthpiece directed downward, a movement apparatus (300) for moving each bell-shaped member (280) in vertical direction between a raised position to a lowered position, a vacuum generating apparatus (340) to reduce the inner volume of bell-shaped members (280), and a plurality of welding elements (390), each of which is contained inside a respective bell-shaped member (280) for airtightly welding the closing film (45) on the glass-shaped body (15) contained in the housing seat (115).