During filming, the cast and crew faced several challenges, including:

The first 9 episodes received mixed reviews from critics and fans, but the show's loyal fan base was disappointed by the abrupt cancellation.

Season 4 of Prison Break was filmed primarily in two phases: (Episodes 1–16) and December 2008 to March 2009 (Episodes 17–22, plus the subsequent movie material). The primary filming location shifted from Dallas, Texas (for the first 16 episodes) to Los Angeles, California (for the final arc).