In 2016, McDonald starred on Broadway as the vaudeville performer Lottie Gee in a new musical titled Shuffle Along, or, the Making of the Musical Sensation of 1921 and All That Followed about the making of the 1921 musical Shuffle Along. Shuffle Along closed on July 24, 2016 and McDonald began a maternity hiatus at that time.
McDonald won the Tony Award for Best Performance by an Actress in a Leading Role in a Play for this role, making her the first person to earn six Tony Award wins for acting (not counting honorary awards) and the first person to win a Tony Award in all four acting categories. In her acceptance speech, "she thanked her parents for encouraging her to pursue her interests as a child." She also thanked the "strong and brave and courageous" African-American women who came before her, saying in part, "I am standing on Lena Horne's shoulders. I am standing on Maya Angelou's shoulders. I am standing on Diahann Carroll and Ruby Dee, and most of all, Billie Holiday. You deserved so much more than you were given when you were on this planet. This is for you, Billie." This performance was filmed at Cafe Brasil in New Orleans and broadcast on HBO on March 12, 2016. McDonald received a 2016 Emmy Award nomination for Outstanding Lead Actress in a Limited Series or Movie for her role in the broadcast.
On September 22, 2016, Audra McDonald was awarded the National Medal of Arts by President Barack Obama for 2015. The Award states, in part: "for lighting up Broadway as one of its brightest stars.... In musicals, concerts, operas, and the recording studio, her rich, soulful voice continues to take her audiences to new heights."