By the late '90s, the complex was in decline. It was revitalized in two stages. The first, done between 2001 and '02, added the aforementioned cinema and Target. A more comprehensive refurbishment began in 2003. The northwest store block was replaced with new Kohl's and Staples stores. BAYFAIR CENTER now encompassed 823,120 leasable square feet and housed eighty-eight stores and services.

The mall  achieved its 60th year in business in 2017. By this time, Staples had been shuttered, with Kohl's expanding into its vacant space. New Jamba Juice and Nubi Yogurt stores (in light gray) were added, covering the old Staples entry. DSW (Designer Shoe Warehouse) has also been installed in the northeast corner of the complex, taking out four store spaces.