John Philemon Paca's adult life centered on landholding and plantation management on Maryland's Eastern Shore. When his father, William Paca, died in 1799, he inherited Wye Hall on Wye Island in Queen Anne's County. In October 1800 he married Juliana Carroll Tilghman, whose inherited Wye Plantation occupied the island's other major estate. Their marriage brought together substantial property, while their household also included children and, at times, members of the wider Paca family.

The plantations depended on enslaved labor. Maryland archival accounts record more than one hundred enslaved people on the Pacas' Wye Island property in successive censuses, with totals changing over time. Archaeological research describes the landscape of fields, workers' quarters, and the large house inherited from the earlier generation. It also notes that John manumitted several enslaved people during his ownership. These individual releases did not end the family's reliance on slavery.

Paca and his wife also held interests beyond Wye Island. In December 1832 they sold four acres of Juliana's land at Turkey Point in Cecil County to the federal government for $564, providing the site for a lighthouse guiding shipping toward the Elk River and the Chesapeake and Delaware Canal. His recorded activities chiefly concern property and family affairs rather than a public career comparable to his father's. After John's death in 1840, Juliana continued to hold the Wye Hall property.