Archival photographs of Lilly House from the 1930s were the starting point for research of interior furnishings. Approximately 90 percent of main-level room furnishings were located, including furniture, fixtures, decorative arts objects and rugs. Many of the second-level bedroom furnishings had been removed and sold in the 1970s, and no archival photographs were found documenting the appearance of these rooms in the 1930s.

The IMA's registration department catalogued approximately 800 objects belonging to Lilly House, and the Museum's conservation laboratory executed condition reports.

Analysis of interior paint layers and wall finishes was done in each of the rooms to determine exact paint colors and wood stain finishes used in the house during the 1930s. All interior paint and stain colors used for the restoration were color-matched to original samples recovered through testing.

IMA historians researched and identified historically appropriate replacements for the few main-level furnishings that were missing or unrecoverable. Fixtures, fabrics, floorings and wall coverings were ordered, including a handpainted wallpaper that is still produced in China in the exact pattern used in the Lilly House drawing room over 70 years ago.

Scenic murals by Canadian artist Douglas Riseborough, which the Lillys commissioned for the house in the 1950s, were conserved.