A judge initially ruled that Guzman would appear in court by video on Friday rather than have marshals escort him to and from a high-security Manhattan jail cell. The order was changed after his lawyers asked the judge to reconsider.
Guzman is charged with running a massive drug trafficking operation that laundered billions of dollars and oversaw murders and kidnappings.
Guzman has repeatedly been imprisoned and escaped in Mexico US authorities have pursued him for years.
To get Mexico to hand him over to the US, prosecutors agreed not to seek the death penalty. They're demanding he forfeit USD 14 billion in assets. Guzman has pleaded not guilty.