The show hasn't run since Disney World reopened in July.
Theme park news: Biden coming to Hall of Presidents / Disney exec pay restored amid mass layoffs / Dorney Park vaccines
Disney did not say how long the Hall of Presidents refurbishment would last.
At full build-out, the $1 billion resort will offer 10,000 bedrooms across a variety of properties.
Travel agents said guests will learn to live without Magical Express when the service ends in 2022.
The unannounced visits determine whether theme parks are complying with Orange County, Florida's rules on face masks and physical distancing.
2021's new attraction lineup ranges from record-setting roller coasters to an immersive hotel experience.
While Central Florida COVID-19 hospitalizations have dropped since their mid-July peak, health experts are still encouraging physical distancing and the use of face masks.
Disney World has kept its water parks closed ever since the initial COVID-19 shutdown in mid-March.