VF-32 deployed once again in November 2000 for the maiden voyage of the USS Harry S. Truman.
They spent four months in support of Operation Southern Watch and returned home on May 23, 2001.
In December 2002 VF-32 deployed once again on Harry S. Truman in support of Operation Noble Eagle and Operation Northern Watch.

In support of Operation Iraqi Freedom (OIF) in 2003, VF-32 was deployed to the Mediterranean Sea aboard Harry S. Truman.
VF-32 flew strike missions and missions in support of US Special Forces on the ground.
VF-32 was involved in the worst friendly fire incident of the war when on 6 April 2003 a squadron F-14 crew was cleared to attack an Iraqi tank near Dibakan, 30 miles (48 km) south east of Mosul.
Instead, they mistakenly dropped a single laser-guided bomb on a vehicle convoy consisting of US Special Forces and Kurdish resistance fighters, killing 18 Kurdish fighters, 4 US soldiers and a BBC translator.
An additional 80 people were wounded.
An investigation following the war found that the pilot had been cleared to drop without the benefit of target coordinates provided by the Forward Air Controller, who was “operating under great stress” at the time.
Overall, VF-32 flew 275 sorties and expended 247 laser-guided bombs and 118 JDAM.
In January 2004 VF-32 became the first operational squadron to attempt the launch of six AIM-54 Phoenix missiles from one aircraft.
A launch such as this had not been attempted since 1972.
Five of the six active radar missiles were successfully launched.
VF-32 returned to NAS Oceana in May 2003.

In 2004 VF-32 deployed again in support of OIF, becoming the first Naval squadron to redeploy in support of OIF.
 The squadron delivered multiple precision guided munitions on insurgent hideouts using the LANTIRN pod in the urban Close Air Support environment.
This would be the squadron's final deployment with the F-14.

In October 2005, VF-32 transitioned to the F/A-18F Super Hornet and in November 2005 the squadron was designated Strike Fighter Squadron Thirty Two (VFA-32).

In November 2007, VFA-32 embarked on USS Harry S. Truman for their first F/A-18F Super Hornet cruise, deploying to the Persian Gulf.
VFA-32 and the rest of CVW-3 returned home on June 4, 2008.
VFA-32 was awarded the Battle Effectiveness Award for maintaining the highest state of battle readiness and sustained superior performance in February 2009.
VF-32 deployed once again in November 2000 for the maiden voyage of the USS Harry S. Truman. They spent four months in support of Operation Southern Watch and returned home on May 23, 2001. In December 2002 VF-32 deployed once again on Harry S. Truman in support of Operation Noble Eagle and Operation Northern Watch.
In support of Operation Iraqi Freedom (OIF) in 2003, VF-32 was deployed to the Mediterranean Sea aboard Harry S. Truman. VF-32 flew strike missions and missions in support of US Special Forces on the ground. VF-32 was involved in the worst friendly fire incident of the war when on 6 April 2003 a squadron F-14 crew was cleared to attack an Iraqi tank near Dibakan, 30 miles (48 km) south east of Mosul. Instead, they mistakenly dropped a single laser-guided bomb on a vehicle convoy consisting of US Special Forces and Kurdish resistance fighters, killing 18 Kurdish fighters, 4 US soldiers and a BBC translator. An additional 80 people were wounded. An investigation following the war found that the pilot had been cleared to drop without the benefit of target coordinates provided by the Forward Air Controller, who was “operating under great stress” at the time. Overall, VF-32 flew 275 sorties and expended 247 laser-guided bombs and 118 JDAM. In January 2004 VF-32 became the first operational squadron to attempt the launch of six AIM-54 Phoenix missiles from one aircraft. A launch such as this had not been attempted since 1972. Five of the six active radar missiles were successfully launched. VF-32 returned to NAS Oceana in May 2003.
In 2004 VF-32 deployed again in support of OIF, becoming the first Naval squadron to redeploy in support of OIF.  The squadron delivered multiple precision guided munitions on insurgent hideouts using the LANTIRN pod in the urban Close Air Support environment. This would be the squadron's final deployment with the F-14.
In October 2005, VF-32 transitioned to the F/A-18F Super Hornet and in November 2005 the squadron was designated Strike Fighter Squadron Thirty Two (VFA-32).
In November 2007, VFA-32 embarked on USS Harry S. Truman for their first F/A-18F Super Hornet cruise, deploying to the Persian Gulf. VFA-32 and the rest of CVW-3 returned home on June 4, 2008. VFA-32 was awarded the Battle Effectiveness Award for maintaining the highest state of battle readiness and sustained superior performance in February 2009.
VFA-32