Schaeffer has written: "In the mid 1980s I left the Religious Right, after I realized just how very anti-American they are, (the theme I explore in my book
Crazy For God)." He added that he was a Republican until 2000, working for Senator John McCain in that year's primaries, but that after the 2000 election he re-registered as an independent.
On February 7, 2008, Schaeffer endorsed Senator Barack Obama for the Democratic Party's presidential nomination, in an article entitled "Why I'm Pro-Life and Pro-Obama." The next month, prompted by the controversy over remarks by the pastor of Obama's church, he wrote: "[W]hen my late father -- Religious Right leader Francis Schaeffer -- denounced America and even called for the violent overthrow of the US government, he was invited to lunch with presidents Ford, Reagan and Bush, Sr."
After the 2008 Russian-Georgian War, Schaeffer described Russia as a resurgent Orthodox Christian power, paying back the West for its support of Muslim Kosovar secessionists against Orthodox Serbia.
On October 10, 2008 a public letter to Senator McCain (and Sarah Palin) from Schaeffer was published in the
Baltimore Sun newspaper. The letter contained an impassioned plea for John McCain to arrest what Schaeffer perceived as a hateful, and prejudiced tone of the Republican party's election campaign. Schaeffer was convinced that there was a pronounced danger that fringe groups in America could be goaded into pursuing violence. "If you do not stand up for all that is good in America and declare that Senator Obama is a patriot, fit for office, and denounce your hate-filled supporters ... history will hold you responsible for all that follows."
Soon after Obama's inauguration, Schaeffer criticized Republican leaders for the course on which they had taken his former party:
How can anyone who loves our country support the Republicans now? Barry Goldwater, William F. Buckley and Ronald Reagan defined the modern conservatism that used to be what the Republican Party I belonged to was about. Today no actual conservative can be a Republican. Reagan would despise today's wholly negative Republican Party.
In February, 2010, Schaeffer criticized President Obama's critics for being racist.