Work on the conservation of the decorative paintings of the Serra Chapel is ongoing since October 2007, with planned completion by May 2008. The conservation team is headed by Debra May and Rachel Burch, of May Painting Conservation, Los Angeles, who specialize in wall painting and easel painting conservation. The work is being carried out alongside team members Leslie Friedman, Traci Lucero, Alice Paterakis and Witold Wojcik. The conservation work was coordinated with the painting of non-decorative wall surfaces by Bay Cal Painting of Oceanside. The project cost a total of $225,000 and was supported by donations given to preserve the Serra Chapel.

The distinctive multicolored ceiling rosettes, carved beams, and wall embellishments visible today were painted in the 1970's to re-create ornamental motifs installed during the 1920's restoration of the chapel by Father St. John O'Sullivan. Because evidence of original painting in the Serra Chapel was fragmentary, the decorations painted in the 1920's were largely based on designs found elsewhere in Mission San Juan Capistrano as well as other California missions. Multiple layers of mineral pigments were applied as washes over new plaster, creating a matte finish that let the texture of the plaster show through.

In the 1970's the decorations were overpainted with modern acrylic paints, resulting in a darker, glossier surface; this effect is heightened where a protective layer of clear polyurethane was also applied. Over the years, various repair and retouching campaigns have been carried out using different paint colors and sheens. By 2007, flaking and peeling paint was evident throughout the chapel, and a layer of dust and grime had accumulated on wall and ceiling surfaces. The decision was made to clean and stabilize the finishes of the 1970's restoration, because it was uncertain if the underlying paint of the 1920's work, the condition of which is unknown, could be successfully revealed and conserved. The scope of the project work was complicated by the presence of lead-containing paint, probably from the 1920's finishes.

Work commenced in the Sanctuary area of the Serra Chapel, where tasks included the cleaning and stabilization of the painted surfaces of the ceiling, walls, and side-altars of the Sanctuary, and was completed in January 2008. The water used to clean some of the surfaces contained detectable traces of lead, and it was necessary to dispose of it in accordance with environmental regulations. Severely flaking paint layers were carefully re-adhered flake by flake by injecting behind individual paint flakes with a conservation-grade adhesive and gently pressing them back down onto the underlying wood or plaster. Areas of lost paint layers were filled and inpainted to mask areas of paint loss, taking care not to impact the original paint layers. Conservation-grade colors were used that can be selectively removed in the future if necessary. Work also involved the repair of numerous damages to the plaster surfaces of the walls and side-altars, the result of wear and tear during the use of the Chapel; these were carried out using natural lime-based repair mortars mixed especially for the project that are compatible with the original materials of construction. These were then inpainted to match adjacent original painted surfaces.

Work continues today on the ceiling beams, ceiling rosettes, and decorative painting of the walls of the main nave of the Serra Chapel, using the same methods and materials that were developed for the Sanctuary. Dramatic cleaning results have been achieved during conservation of the ceiling beams and side altars, and flaking paint on the walls, ceiling beams and rosettes has been successfully re-adhered.