After retiring from UW, he returned to San Francisco, where he co-founded (with William Andereck) the Program in Medicine and Human Values at Sutter Health's California Pacific Medical Center in 2003.
In 1979, Jonsen was appointed to the successor body, the President's Commission on the Study of Ethical Problems in Medicine (1979–82) which devised reports on brain death, foregoing life-support, informed consent and other topics which have become the main subjects of bioethics.
After his retirement from UW, Jonsen returned to his native San Francisco, where he joined his good friend and colleague, William Andereck in co-founding The Program in Medicine and Human Values at Sutter Health's California Pacific Medical Center in 2003.
At Sutter Health's Bioethics Program, he continued his scholarly work and conducted multiple research studies and authored several books and papers.
At the time of his death, Jonsen had completed work on the 9th edition of his book, Clinical Ethics, with co-authors Mark Siegler, William Winslade, and Associate Editor, Ruchika Mishra.
In 2017, The Hastings Center granted Jonsen the most prestigious honor in the field of bioethics, the Henry Knowles Beecher Award for Contributions to Ethics and the Life Sciences.