The so-called "bid books" run to several hundred pages and represent the cities' master plans of venues, budgets, financial guarantees, security, accommodations, transportation and other key aspects of the multi-billion-dollar projects.
The files will be released publicly by the bid cities Tuesday.
The IOC's evaluation commission, headed by Craig Reedie of Britain, will visit the cities in March and prepare a report for IOC members before a meeting with the bidders in Lausanne in July. The full IOC will select the host city in a secret ballot in Buenos Aires on Sept. 7.
The 2020 field initially included six candidates, but Rome dropped out when the Italian government refused to offer financial support, and the IOC cut Doha, Qatar, and Baku, Azerbaijan, from the list last year.
The mayors of Madrid and Istanbul joined their bid teams for Monday's ceremonial handover. Tokyo brought soccer star Homare Sawa, the FIFA women's player of the year in 2011.
Istanbul came up short for 2000, 2004, 2008 and 2012. Madrid finished third for the 2012 Games and second for 2016. Tokyo, which hosted the 1964 Olympics, was third in the voting for 2016.
Tokyo received the highest praise in an IOC technical report last year that said the Japanese bid presents "a very strong application." Madrid has a "strong application," while Istanbul's project "offers good potential," the report said.
British bookmaker William Hill listed Tokyo as the 4-6 favorite, with Istanbul at 5-2 and Madrid at 3-1.
While Tokyo is seen as a safe choice, Istanbul holds the emotional pull of representing a new destination for the Olympics, a key factor in recent host city votes.
The IOC is taking the 2014 Winter Games to the Russian city of Sochi, the 2016 Olympics to Rio de Janeiro and the 2018 Winter Games to Pyeongchang, South Korea. Istanbul, which straddles both Europe and Asia, would take the games to a predominantly Muslim country for the first time.
"This is a new bid for a new Turkey," Istanbul bid leader Hasan Arat told The Associated Press in a telephone interview from Lausanne. "This time we are not in the same position as our four previous bids. This is the latest step in a journey that is taking five bids and nearly two decades. We experienced, we listened and we learned."
All three bids face geopolitical and economic challenges.
Spain is in the throes of its second recession in just over three years, with its economy battered by a collapse in the real estate sector and unemployment as high as 25 percent. Madrid bid leaders say most of their venues are already built and the Olympics could serve as a catalyst for economic recovery.
Japanese leaders have said hosting the Olympics in Tokyo would serve a symbol of recovery from the disastrous earthquake and tsunami in 2011. Japan has also been in a nasty dispute with China over a cluster of islands in the East China Sea and has just undergone a change in government that brought Shinzo Abe to power as prime minister.
Istanbul's Olympic bid had previously been compromised by Turkey's desire to host the European soccer championship in 2020. That became moot when UEFA decided to spread the tournament across the continent.
Istanbul is seeking the Olympics at a time when Turkey is in conflict with Syria. Turkey is a former ally of Syria but turned against President Bashar Assad's regime over its violent crackdown on dissent in the nearly 2-year-old civil war that has left 60,000 dead. Turkey is supporting the Syrian opposition and rebels and is providing shelter to some 150,000 refugees.
"This is a global issue," Arat said. "This does not really affect our bid and our future plans. Turkey is a unique example of a secular democracy."