The second excavations were done in the winter of 2000-2001 before reconstruction of the Wing began, and the winter of 2008-2009 as the reconstruction drew to a close. It involved several areas, which had not been examined in the first excavations, and were to be impacted by construction-related activities.

In 2000-2001, excavations took place to prepare for a new drainage system to be installed beneath the Wing by the Poplar Forest restoration team. These excavations were located beneath the original floor brick and in the vicinity of a Jefferson-era wall that supported the colonnade for Wing of Offices. Archaeologists found a variety of Jefferson-era artifacts, which included ceramic sherds, nails, animal bone, bottle glass, and a fork from Jefferson's era along with artifacts from later periods.

They also found a thin layer of charcoal and hearth debris in front of the kitchen fireplace. A thicker layer filled with chipped stone, which may mark where the ground surface was when Jefferson's masons built the original chimney stack for the Wing’s kitchen was also recovered. Samples of charcoal and other burned material were recovered from the hearth for laboratory analysis. In addition, archaeologists searched for the evidence of planting holes and other landscaping features in order to collection additional information about the landscape of Poplar Forest before and after the construction of Jefferson’s east mound.

In 2008-2009, excavations occurred north of Jefferson’s Wing of Offices for a visitor’s handicap lift and stairway. During the excavations, archaeologists located several planting features and a small posthole, which date to Jefferson’s time or more recent periods. A wide variety of artifacts were recovered. The most intriguing were sherds of Jefferson-era black basalt and a large number of hand-made wrought iron nails. These nails were found in a layer of soil, which contained brick and charcoal flecks and could be destruction debris from the original Wing, or main house, after a fire in 1845.  Other artifacts that were reflected the use of the detached kitchen and smokehouse that was built after the Wing was torn down. These included flow blue ceramics and chimney glass from a kerosene lamp.