Embodiments generally relate to vial preparation methods and to vials prepared by such methods. Some embodiments relate to use of an apparatus, such as a lyophilisation apparatus, to perform the methods. An illustrative vial preparation method comprises: housing a plurality of vials in a temperature-controlled environment, wherein the plurality of vials each have a volume of a substance therein and each defines an unfilled volume therein, each vial having a stopper partially inserted into an opening of the vial so that gas can transfer between the unfilled volume and an external volume; applying a vacuum to the environment to reduce pressure in the environment and in the unfilled volume of each vial to a first pressure level; venting an inert gas into the environment to raise the pressure in the environment and in the unfilled volume of each vial to a second pressure level; allowing the vials to rest in the environment at the second pressure level for a predetermined period; repeating the applying, venting and allowing at least once; and fully inserting the stopper into each opening to seal each vial after the repeating.