Provided is a loading tray assembly for housing a lyophilization container and a related system and method. The loading tray assembly includes a chassis including a contact void configured to facilitate direct contact between the attached lyophilization container and a lyophilizer shelf. The method includes securing a multi-part lyophilization container including a peelable seal on a lyophilization loading tray assembly, inputting a liquid into a non-breathable section of the lyophilization container, loading the tray assembly into a lyophilizer, freezing the liquid, applying heat energy and a vacuum, the vacuum causing an opening of the peelable seal and occluding the lyophilization container to isolate the frozen liquid.