Launch from Cape Canaveral (KSC); landing 735 km southeast of Pogo-Pogo- slands in the Pacific Ocean.

Thirty-six-and-a-half seconds after lift-off, the vehicle triggered a lightning discharge through itself and down to the earth through the Saturn's ionized plume. Protective circuits on the fuel cells in the service module falsely detected overloads and took all three fuel cells offline, along with much of the CSM instrumentation. A second strike at 52 seconds after launch knocked out the "8-ball" attitude indicator. The telemetry stream at Mission Control was garbled. However, the Saturn V continued to fly correctly; the strikes had not affected the Saturn V's Instrument Unit.

This mission marked the second manned lunar landing. After landing in Ocean of Storm Charles Conrad and Alan Bean performed several scientific work on the lunar surface. When Charles Conrad, who was somewhat shorter than Neil Armstrong, stepped onto the lunar surface, his first words were "Whoopie! Man, that may have been a small one for Neil, but that's a long one for me." This was not an off-the-cuff remark: Charles Conrad had made a $500 bet with reporter Oriana Fallaci he would say these words, after she had queried whether NASA had instructed Neil Armstrong what to say as he stepped onto the Moon. Charles Conrad later said he was never able to collect the money.
The astronauts deployed an S-band antenna, solar wind composition experiment, the American flag and most important, the Apollo Lunar Surface Experiments Package (ALSEP) with a SNAP-27 atomic generator. This was done during the first EVA on November 19, 1969 (3h 56m). To improve the quality of television pictures from the Moon, a color camera was carried on Apollo 12 (unlike the monochrome camera that was used on Apollo 11). Unfortunately, when Alan Bean carried the camera to the place near the lunar module where it was to be set up, he inadvertently pointed it directly into the Sun, destroying the SEC tube. Television coverage of this mission was thus terminated almost immediately.

The second EVA was performed on November 20, 1969 (3h 49m) in which different samples were collected and photographic panoramas were obtained. Apollo 12 successfully landed within walking distance of the Surveyor 3 probe, which had landed on the lunar surface on April 20, 1967. Charles Conrad and Alan Bean removed pieces of the probe to be taken back to Earth for analysis. It is claimed that the common bacterium Streptococcus mitis was found to have accidentally contaminated the spacecraft's camera prior to launch and survived dormant in this harsh environment for two and a half years. However, this finding has since been disputed: see Reports of Streptococcus mitis on the Moon. All in all 34,4 km of material gathered.

After 31,5 hours on the lunar surface launch to the Command Module Yankee Clipper with Richard Gordon in the moon orbit. Richard Gordon had completed a lunar multispectral photography experiment and photographed proposed future landing sites during that time. Intrepid's ascent stage was dropped (per normal procedures) after Charles Conrad and Alan Bean rejoined Richard Gordon in orbit. It impacted the Moon on November 20, 1969 at 3.94°S 21.20°W. The seismometers the astronauts had left on the lunar surface registered the vibrations for more than an hour.

The crew was recovered by the USS Hornet.