In May 1992, Duque was selected to join the Astronaut Corps of the European Space Agency (ESA) based at the European Astronauts Centre (EAC) in Cologne, Germany. In 1992 he completed the Introductory Training Program at EAC and a four-week training program at TsPK (the Russian Astronauts Training Centre) in Star City, Russia, with a view to future ESA-Russian collaboration on the Mir Space Station. From January to July 1993, he performed Basic Training at EAC.
In August 1993, Duque returned to TsPK to train for the joint ESA-Russian Euromir 94 mission and the following May was selected as member of Crew 2 joining Yuri Gidzenko and Sergeij Avdeev. During Euromir 94, which took place from 3 October to 4 November 1994, he was the prime Crew Interface Coordinator (CIC) in the Russian Mission Control Centre (TsUP). He served as the main contact with fellow ESA astronaut Ulf Merbold onboard Mir and was the coordinator between Mir, the Euromir 94 Payload Operations Control Centre (SCOPE) in Toulouse, France, and the project management.
In January 1995, Duque began an extended training course on Russian space systems in Star City and supported the second joint ESA-Russian mission, EUROMIR 95.
Duque reported to the Johnson Space Center in August 1996 for two years of training and evaluation. In August 1996, Duque entered the Mission Specialist Class at NASA/Johnson Space Centre in Houston. This training led to his certification as mission specialist in April 1998. He was selected in November 1997, to fly as Mission Specialist on the STS-95 mission scheduled for October 1998. He was initially assigned to the Computer Support Branch of the Astronaut Office, supporting Space Shuttle and International Space Station Programs and advanced technology development.
Mir Expedition EO-20. Crew commander was Yuriy Pavlovich Gidzenko of the Russian Air Force. Flight engineer was Sergey Vasilyevich Avdeev of RKK Energiya, and cosmonaut-researcher was Thomas Reiter of the European Space Agency. Soyuz TM-22 docked with Mir's front (-X) port at 10:29:54 GMT on September 5 and the hatch was opened at 11:01:23. On February 29 the crew undocked from Mir in Soyuz TM-22, and at 10:42 GMT they landed in Kazakhstan.
The flight of STS-95 provoked more publicity for NASA than any other flight in years, due to the presence of ex-astronaut Senator John Glenn on the crew, which also included the first Spanish astronaut, Pedro Duque. The US Navy PANSAT student satellite was deployed on Oct 30 into a 550 km x 561 x 28.5 degree orbit. The Spartan 201 satellite was deployed from Discovery on November 1 and retrieved on November 3. Spartan 201 was on its fifth mission to observe the solar corona. The data on this mission would be used to recalibrate the SOHO satellite which recently resumed observation of the Sun following loss of control. Discovery landed at 17:03:31 GMT November 7 on Runway 33 at the Shuttle Landing Facility at Kennedy Space Center.