When she reemerged in 1995 with the album The Secret Is Out, she stayed on top of new currents in black popular music and incorporated them into her sound. Increasingly asserting control over her own music, she handpicked the producer for the new album, the Charlotte, North Carolina-based gospel impresario John P. Kee, known as "The Prince of Gospel," whose album The New Life Community Choir Featuring John P. Kee was one of the biggest gospel records of the middle of the decade.

The album featured an even wider stylistic mix than Armstrong had previously attempted. "It's traditional and churchy, but also hip-hop," she told Billboard. "There's the blues ... classical ... he's [Kee] just exploring my talent and challenging me all the way." Such tracks as the hip-hop-inflected "Love Lifted Me" earned Armstrong a place, along with Yolanda Adams and CeCe Winans, in a 1996 Essence magazine feature on the "divas of gospel." A reviewer for American Visions seemed both attracted and unnerved by the new energy of Armstrong's style: "I'm almost afraid to say it, but she does indeed belt out her music with such conviction that the line between gospel and contemporary is blurred. But the meaning is the same: salvation."

Indeed, even as she continued to break new ground, Armstrong reaffirmed her commitment to gospel traditions. She questioned some of her label's more blatant efforts to cross her over to a secular audience, observing to Billboard, "They were trying to direct me into the secular market, and they just lost me. Fans were wondering, 'What's up, you're going secular.' But I never left. I'm gospel, and I'm not going anywhere." She continued to exert influence over secular artists--it was said that vocal diva Mariah Carey studied her singing--but she would close out the 1990s with a spectacular return to gospel basics. In 1998 Armstrong recorded Desire of My Heart--Live, recorded at the Perfecting Church in her hometown of Detroit. The album was released on the Verity label, and its release was accompanied by a video made as it was being recorded. Desire of My Heart--Live marked a homecoming and a moment of renewal for Armstrong in several ways. She wrote the album's title track, the first time one of her own compositions had been included on one of her releases, and she served as the album's co-producer. Armstrong's father, Elder Jesse Bell, was featured on the track "Labor in Vain," and Perfecting Church pastor Marvin Winans joined Armstrong and the church's choir on the barn-burning "He Is Lord." Billboard called the album "an enduring classic." Reflecting on her unheralded influence on gospel music the magazine observed, "It took a while, but the world seems to be catching up to Armstrong." Her second greatest-hits release, which appeared on Verity in 1999, gave gospel listeners the chance to survey the development of her immensely important career.