Although Lindner was a devout Baptist he was considered as one of the largest non-Jewish donors to the organized Jewish community in the United States. In 1978 he was named the Man of the Year by the United Jewish Appeal, and was later named a recipient of the Tree of Life Award for the Jewish National Fund, and was recognized as the largest non-Jewish purchaser of Israel Bonds. Lindner, who said an early loan from Isaac Wolfson inspired him to never forget his gratitude to the Jewish people, donated to such causes in multiple occasions, including $1 million in a 1991 fundraiser and $5 million in 2004.

Whereas the Lindner companies and financial institutions once operated on conservative, cautious principles they later became involved in riskier ventures. Lindner insurance companies began to invest in Jun K bonds and other Lindner companies began to issue Jun K bonds. The SEC noted that Lindner companies were the single largest filers of new issues of securities in the U.S. Lindner was repeatedly accused of self-dealing in the corporations under his control; e.g., having such a corporation give him a private aircraft. He became closely associated with Michael Milken and the others in the Jun K bond field to the extent that his financial institutions invested in the Jun K bonds of the others. He and others actively engaged in public relations efforts to present an image of fiscal propriety to the general public while helping to bankrupt individuals and families aiding Central American democracy groups in the 1980s even while they helped Chiquita's cause.

Lindner supported the Republican Party. During the 2004 election, the Lindner family contributed tens of thousands of dollars to Republicans, including the Republican National Committee and several politicians. In 2004, the Republican National Committee named Lindner as one of 62 "Super Rangers", the highest level of fundraising recognition, accorded to those who raise $300,000 or more. Lindner, an ally of George W. Bush, secured the use of Great American Ball Park for Bush's re-election campaign on October 31, 2004, two days before the 2004 Presidential Election.

In 2005, Lindner was among 53 entities that contributed the maximum of $250,000 to the second inauguration of President George W. Bush.

Carl Lindner Jr. died on October 17, 2011, at age 92. He is survived by his wife, the former Edyth Bailey; his sons, Carl III, Craig and Keith; 12 grandchildren; and 6 great-grandchildren.