A biopsy device includes a probe, a holster, and a tissue sample holder for collecting tissue samples. The probe includes a needle and a hollow cutter. The tissue sample holder includes a housing having one or more chambers that are configured to receive a removable tray including one or more prongs and a bulk chamber of a different volume than the one or more chambers. The housing is releasably engageable with the probe. Each tray prong is configured to receive a tissue sample communicated through the cutter lumen. The tray is removable from the housing, such as along an axial direction. The tissue sample holder is rotatable to successively index each chamber to the cutter lumen. The trays may be flexible, resilient, or rigid.