In 1893, descendants of John Bartram formed the John Bartram Association to assist the City of Philadelphia with preservation of the site. Today, it is operated as a museum and public garden by the Association in cooperation with the Fairmount Park Commission.

Restoration of the grounds and buildings is an ongoing process always preceded by historical research and archaeological investigation. Restoration projects have included rescuing the buildings from disrepair, reclaiming an adjacent industrial tract as a wildflower meadow, enriching the botanical garden with native plant species from the Bartram period, hand excavating and replanting Bartram's 18th century "fish pond" and creating the first interpretive wetland on the lower Schuylkill River.

The John Bartram Association hosted a Tercentennial Celebration in 1999, to commemorate the 300th anniversary of the birth of John Bartram. (Photograph at left of 1893 John Bartram Association and Family Reunion at Bartram's Garden.)