During George H. W. Bush's presidency, Zoellick served with Baker, by then Secretary of State, as Under Secretary of State for Economic and Agricultural Affairs, as well as Counselor to the Department (Under Secretary rank). In August 1992, Zoellick was appointed White House Deputy Chief of Staff and Assistant to the President. Zoellick was also appointed Bush's personal representative for the G7 Economic Summits in 1991 and 1992.
During 1999 Zoellick was, for a short period, the head of the Center for Strategic and International Studies (CSIS)
Zoellick played a key role in the U.S.-W.T.O. dispute against the European Union over genetically modified foods. The move sought to force genetically modified crops and food on the E.U., which would not otherwise accept them, or be slow to do so..
On January 7, 2005, Bush nominated Zoellick to be Deputy Secretary of State. Zoellick assumed the office on February 22, 2005. The New York Times reported on May 25, 2006 that Zoellick could soon announce his departure. Zoellick agreed to serve as Deputy Secretary of State for not less than one year. He was seen as a major architect of the Bush administration's policies regarding China.
On September 21, 2005, Zoellick created a major stir on both sides of the Pacific by giving a remarkably candid speech to the National Committee on U.S.-China Relations. In the speech, he not only introduced the notion of China as a "stakeholder" in the international community but sought to allay fears in the US of ceding dominance to China. The full text of his speech can be found here.
In addition, Zoellick chartered a new direction in the Darfur peace process. During a trip to a Darfur refugee camp in 2005, he wore a bracelet with the motto, "Not on our watch." Zoellick was seen by many as the administration's strongest voice on Darfur. His resignation catalyzed groups, such as the Genocide Intervention Network, to praise his record on human rights issues.
Tom Barry, the policy director of the International Relations Center, has written that Zoellick "regards free trade philosophy and free trade agreements as instruments of U.S. national interests. When the principles of free trade affect U.S. short-term interests or even the interests of political constituencies, Zoellick is more a mercantilist and unilateralist than free trader or multilateralist.
Gavan McCormack has written that Zoellick used his perch as U.S. trade representative to advocate for Wall Street's policy goals abroad, as during a 2004 intervention in a key privatization issue in Japanese Prime Minister Junichiro Koizumi's re-election campaign. McCormack has written , "The office of the U.S. Trade Representative has played an active part in drafting the Japan Post privatization law. An October 2004 letter from Robert Zoellick to Japan’s Finance Minister Takenaka Heizo, tabled in the Diet on August 2, 2005, included a handwritten note from Zoellick commending Takenaka. Challenged to explain this apparent U.S. government intervention in a domestic matter, Koizumi merely expressed his satisfaction that Takenaka had been befriended by such an important figure… It is hard to overestimate the scale of the opportunity offered to U.S. and global finance capital by the privatization of the Postal Savings System.
In a January 2000 Foreign Affairs essay entitled "Campaign 2000: A Republican Foreign Policy," he was one of the first of those now associated with Bush's foreign policy to invoke the notion of "evil," writing: "[T]here is still evil in the world — people who hate America and the ideas for which it stands. Today, we face enemies who are hard at work to develop nuclear, biological, and chemical weapons, along with the missiles to deliver them. The United States must remain vigilant and have the strength to defeat its enemies. People driven by enmity or by a need to dominate will not respond to reason or goodwill. They will manipulate civilized rules for uncivilized ends." The same essay praises the "idealism" of Theodore Roosevelt and Woodrow Wilson. Two years earlier, Zoellick was one of the signatories (who also included Donald Rumsfeld, Paul Wolfowitz, Richard Perle, Elliott Abrams, Zalmay Khalilzad, John R. Bolton, Richard Armitage, and Bill Kristol) of a January 26, 1998 letter to President Bill Clinton drafted by the Project for the New American Century calling for "removing Saddam [Hussein]'s regime from power."
While in the position of Deputy Secretary of State, Zoellick visited Sudan four times. He supported expanding a United Nations force in the Darfur region to replace African Union soldiers. He was involved in negotiating a peace accord between the government of Sudan and the Sudan Liberation Army, signed in Abuja, Nigeria in May 2006.
Zoellick is considered an influential advocate of US-German relations. Fluent in German, he possesses considerable knowledge of Germany, the country of his family background.