The Dutchman will leave his post when his current contract expires in December.
The 54-year-old stated before the London 2012 Olympics that he would walk away if Team GB failed to meet a target of at least eight medals, including one gold. The team fell two short, even if four of the six medals were gold.
UK Athletics had been prepared to offer van Commenee a new contract, but he has decided to keep his promise to quit.
Immediately after the Olympics, the ambitious coach said he thought it was "weird" that so many people wanted him to stay despite his team falling short.
Speaking today, he said: "Whilst I am thankful for the kind comments and wishes I have received in recent weeks, I believe my decision has the interests of British athletics at its heart in sustaining this culture."