A biopsy device comprises a body, a needle, a cutter, and a tissue sample holder. The tissue sample holder comprises an outer cup and a cap. A tray retains severed tissue samples from a biopsy procedure. In some versions, the tray is selectively detachable from the cap in a one-handed operation by the user. The tray may be ejected into a sample container, such as a formalin cup. The cap may include a threaded portion that is configured to engage a complementary threaded portion of a sample container to seal the sample container once the tissue samples have been transferred to the sample container from the tissue sample holder of the biopsy device. One or more ports may be provided in the cap to manage excess fluid within the outer cup of the tissue sample holder, and/or to provide integrated access for a marker delivery device.