The original logo of the mall was a 3-toned rainbow which was red, orange, and yellow, and a font in Dynamo displaying ‘plaza bonita’.

[7] 2000s In mid-2002, the mall went through several phases of renovations, in which the brick exterior and interior was plastered with stucco then painted and had new ceramic tile installed.

In mid-2006, the former Wards store, which had been the location of seasonal retailers (Halloween costumers and art shows) was stripped and gutted and a new plan was announced to the public that the south end of the mall would be demolished and rebuilt.

[8] In 2008 the newly renovated part of the mall had opened with additional anchors including Target, Borders (which had moved from Otay Ranch Town Center), and AMC Theatres as well as close to 40+ new shops like H&M, a new food court known as the Dining Terrace, as well as a three floor parking structure.

[15] Many non-essential stores had been affected by the pandemic such as John's Incredible Pizza Company which did not reopen in the re-opening of Plaza Bonita in May 2021[16] and later was gutted by June 2021.

[17] In the summer of 2022, Japan's Round 1 Bowling & Amusement planned to open its first San Diego location at Westfield North County this later changed to Plaza Bonita in September when the Round One Corporation website released the Plaza Bonita location would be 'coming soon', replacing the former Johns Incredible Pizza's space.