She next starred in the musical adaptation of Neil Simon's The Goodbye Girl with music by Marvin Hamlisch (1993). Peters won her second Tony for her performance as Annie Oakley in the 1999 revival of Annie Get Your Gun opposite Tom Wopat. Among many glowing notices for this role, critic Lloyd Rose of the Washington Post commented: "[Peters] banishes all thoughts of Ethel Merman about two bars into her first number, 'Doin' What Comes Natur'lly.' Partly this is because Merman's Annie was a hearty, boisterous gal, while Peters plays an adorable, slightly goofy gamine... For anyone who cares about the American musical theater, the chance to see Peters in this role is reason enough to see the show." Playbill went even further: "Arguably the most talented comedienne in the musical theatre today, Peters manages to extract a laugh from most every line she delivers."

In 2003, Peters took on the role of Mama Rose in the Broadway revival of Gypsy, earning another Tony nomination. Ben Brantley in his New York Times review wrote, "Working against type and expectation under the direction of Sam Mendes, Ms. Peters has created the most complex and compelling portrait of her long career, and she has done this in ways that deviate radically from the Merman blueprint." Arthur Laurents said: "But in 2003 there was a new Rose on Broadway: Bernadette Peters! Brilliant, original, totally unlike any of the others." In February 2006, she participated in a reading of the Sondheim-Weidman musical Bounce. On September 24, 2007, Peters participated in a one-time only charity reading of the play Love Letters with her former Gypsy co-star, John Dossett.

After an absence from the Broadway stage of six years (Gypsy closed in 2004), she is starring in the Broadway revival of Sondheim's A Little Night Music, as Desiree Armfeldt, beginning on July 13, 2010. She replaced Catherine Zeta-Jones in the role. The New York Times reviewer wrote of her performance, "for theater lovers there can be no greater current pleasure than to witness Bernadette Peters perform the show’s signature number, "Send In the Clowns," with an emotional transparency and musical delicacy that turns this celebrated song into an occasion of transporting artistry. I’m not sure I’ve ever experienced with such palpable force – or such prominent goose bumps – the sense of being present at an indelible moment in the history of musical theater."

Peters is scheduled to play the role of Sally Durant Plummer in the Kennedy Center for the Performing Arts production of another Sondheim musical, Follies, which is to run at the Eisenhower Theatre from May 7 through June 5, 2011. In discussing this casting, the Washington Post theatre critic noted that "The hiring of Peters, a two-time Tony winner and one of Sondheim's favorite actors ... raises expectations that the show will proceed to Broadway."

Peters has been nominated for the Tony Award seven times and won twice. She has also been nominated for the Drama Desk Award eight times and won three times (Annie Get Your Gun, Song and Dance, and Dames at Sea).

Peters was nominated for Emmy Awards for her guest-starring roles on The Muppet Show (1977) and Ally McBeal (2001). She was also nominated for a Daytime Emmy Award, Outstanding Performer in a Children's Special, for her work in the 2002 made-for-television movie Bobbie's Girl. She won the 1987 "CableACE Award" for her role as Dot in the television version of Sunday in the Park With George.

She has appeared in many variety shows with stars such as Sonny and Cher and George Burns. She has both performed and presented on the Academy Awards broadcasts in 1994, 1987, 1983, 1981 and 1976. Peters has been a presenter at the annual Tony Awards ceremony and co-hosted the ceremony with Gregory Hines in June 2002. She also hosted Saturday Night Live in November 1981. She made 12 guest appearances on The Carol Burnett Show as well as appearing with Burnett in the made-for-television version of Once Upon a Mattress and the 1982 film Annie. She also performed at the Kennedy Center Honors ceremony for Burnett in 2003. Peters often appeared on the Tonight Show Starring Johnny Carson and on the day-time talk show Live with Regis and Kelly, both as a co-host and a guest. Peters voiced stray cat Rita in the Rita and Runt segments of the animated series Animaniacs. Rita often sang on the show, sometimes in parodies of songs from Broadway musicals. She appeared on Inside the Actor's Studio in November 2000, discussing her career and craft.

Peters has co-starred in a number of television movies, including The Last Best Year (1990) with Mary Tyler Moore, Rodgers and Hammerstein's Cinderella (1997) with Brandy (receiving a nomination for the "Golden Satellite Award" for her role), and Prince Charming (2003) with Martin Short. She co-starred in her own television series, All's Fair, with Richard Crenna in 1976–77, for which Peters was nominated for a Golden Globe award as Best TV Actress — Musical/Comedy. In March 2005, she made a pilot for an ABC situation comedy series titled Adopted, co-starring with Christine Baranski, but it was not picked up. Peters appeared in the Lifetime television movie Living Proof which was first broadcast on October 18, 2008. She played the role of Barbara, an art teacher with breast cancer, who is initially reluctant to participate in the study for the cancer drug Herceptin. Andrew Gans of Playbill wrote, "Peters is able to choose from an expansive emotional palette to color the character, and her performance... is moving, humorous and ultimately spirit-raising".

Peters' television work in recent years also includes guest appearances on several television series. She appeared as the sharp-tongued sister of Karen Walker (Megan Mullally) on the penultimate episode of the NBC series Will & Grace, "Whatever Happened to Baby Gin?" (May 2006); as a defense attorney on the NBC series, Law & Order: Special Victims Unit (November 2006); as a judge on the ABC series Boston Legal (May 2007); and as an accident victim in Grey's Anatomy (September 2008). Of her role in Grey's Anatomy, TV Guide wrote: "Peters is especially fine as she confronts a life spinning out of control. I'd make her an early contender for a guest-actor Emmy nomination." In January, February and May 2009, she appeared in the ABC series Ugly Betty in five episodes as Jodie Papadakis, a magazine mogul running the YETI (Young Editors Training Initiative) program that Betty and Marc are in.