The shop, in Stratford, will sell Olympic merchandise and become the 26th home-grown sponsor.
An estimated 10,000 licensed products which will be on sale.
The john Lewis Flagship store in Oxford Street will also stock the memorabilia.
The net profit on the merchandise will be pumped back into Olympic coffers
John Lewis managing director Andy Street said: “Sustainability and community are at the heart of our business and we are therefore delighted to be involved with the regeneration of east London through anchoring the Olympic development in Stratford with our latest full-line department store as well as helping to fund the most exciting sporting event for a generation.”
The company is also bankrolling some Olympic coaches as well as seven sporting hopefuls from the capital.
London 2012 chairman Lord Coe said: "They are a great British brand with a reputation for first class customer care and excellence.
"They supported us during the bid and so it is fantastic to have them on board as a sponsor.
"They bring a wealth of retail experience which will be invaluable to us as our merchandise programme ramps up and crucially, members of their staff will join our own to provide expertise and ensure those visiting our Games receive the warmest of welcomes in 2012."
Games organisers have been set a £2bn target of fundraising from the private sector.