Progress M1-11 carried supplies to the International Space Station, including food, water and oxygen for the crew and equipment for conducting scientific research. Its cargo included an Orlan spacesuit, a replacement flex hose for the Destiny module, a new Elektron oxygen generator with spare parts for the Elektrons already aboard the ISS, some oxygen generator candles, spare batteries, new fire detection and suppression systems, a gas analysis system, cameras, data cassettes, and an external experiment package for the Zvezda module, Matryoshka. It was also used to perform a reboost maneuver shortly before its departure from the ISS.
It remained docked for four months before undocking at 09:19:29 UTC on May 24, 2004 to make way for Progress M-49. Following undocking, it remained in orbit for ten days, conducting tests of its attitude control system. It was deorbited at 09:50 UTC on June 03, 2004. The spacecraft burned up in the atmosphere over the Pacific Ocean, with any remaining debris landing in the ocean at around 10:36:25 UTC.

The only EVA in this mission was performed by Michael Foale and Aleksandr Kaleri on February 26, 2004 (3h 55m) to install new experiments and replace and remove parts for existing experiments on the exterior of the ISS. The EVA was shortened due of cooling problems with Aleksandr Kaleri's space suit.
Michael Foale and Aleksandr Kaleri were able to complete a number of their tasks. The first task was the replacement of cassette containers that hold sample materials for an experiment studying the effect of long-duration exposure to the microgravity environment. Later, Michael Foale replaced two similar cassettes housed on the outside of the Zvezda Service Module. A Russian experiment named Matryoshka was attached to the outer hull of Zvezda which will provide data on radiation exposure to the human body during space flight. The spacewalkers also removed one of the suitcase-sized devices associated with the Japanese Aerospace Exploration Agency's MPAC-SEEDS experiment. They relocated a second device. This experiment was studying micro-meteor impacts and material exposure in the space environment. This experiment was installed on the ISS by Expedition 3 spacewalkers October 15, 2001. The crew was not able to complete the removal of laser light retroreflector devices from the aft end of Zvezda. The reflectors were being studied as navigation devices for the European Space Agency's Automated Transfer Vehicle, which first flew to the ISS in 2008. Another task not included was work on a materials science experiment called Kromka. This experiment measured the amount of residue emitted from Zvezda's jet thruster firings.
The crew conducted the first two-person spacewalk at the International Space Station. Unlike previous spacewalks conducted by ISS crews, there was not a crewmember inside the Station as the spacewalkers worked outside. The spacewalk was based out of the Pirs docking compartment. The spacewalkers wore Russian Orlan space suits.

Among other repair work the crew later repaired successful a treadmill and an oxygen producing Elektron unit aboard the ISS. The crew also performed all in all 27 experiments on different scientific fields.