The mall was developed in 1976 by the Homart Development Company and originally had wood and glass railings and an overall off-white and brown theme. The pillars in the mall were made of white pebbles. There was no elevator in the mall and originally the mall featured a large ramp for access to the second floor by wheelchair. The mall was designed with a sunken basement-level foodcourt. The mall featured the department stores Powers Dry Goods and Sears. Powers' store became Donaldson's in 1985, then Carson Pirie Scott in 1987. Later, a Target store was constructed adjacent to the mall and connected by a walkway.
The mall underwent a major renovation and the color scheme was changed to a pink and aqua pastel theme. The white pebble pillars were covered with pastel aqua round casings. The ramp was removed and replaced with a free standing elevator. The glass and wood railings were replaced with aqua painted metal. The food court was decorated with large neon palm trees and given a fountain that changed colors. The Carson Prairie Scott store became a Mervyn's California, and work began on adding a Kohl's department store. A second United Artists movie theater was built, called "Eden Prairie East" and the old theater located beneath the Target walkway was renamed "Eden Prairie West". The mall entrances at this time had large white pyramids.
The mall underwent the most major renovation in 2001. A new wing was added to the mall and the floor plan changed considerably to make the mall more modern and upscale. The food court was moved out of the recessed basement, which has been sealed in and now serves as the mall offices and other offices, changing the mall's store layout from a three-story mall to two stories. A large AMC movie theater was added to the mall and the two United Artists theatres have closed. The Target expanded into a Target Greatland and connected to the mall, replacing the old walkway. A Von Maur department store was added to the mall, the mall entrance utilizing space that had been smaller mall stores near the old food court area. The mall has a simplified stylized "EP" logo to replace the older handwritten style logo, and the pastel theme disappeared in favor of wood and stonework. After the Mervyn's California went out of business in 2003, Department Store Discounters had a brief stay in the Mervyn's location in 2005. JCPenney opened a new store in the former Mervyn's location in March 2007. The current department stores in the mall are JCPenney's, Kohls, Sears, Target, and Von Maur. In October 2013 General Growth Properties sold the mall to Cypress Equities for a reported $99M.
The mockumentary Drop Dead Gorgeous has a scene filmed in the parking lot of the Eden Prairie Center, when they are allegedly parking in the parking lot of the nearby Mall of America. (The Eden Prairie water tower with clock is clearly visible in the background).