When Mitch Zeller takes over Monday as the nation’s top tobacco regulator, it will mark a homecoming of sorts.

Zeller spent much of the 1990s at the Food and Drug Administration spearheading its burgeoning tobacco-control efforts — including pressing Congress to give the agency broader regulatory powers and designing the first nationwide program to keep tobacco out of the hands of minors.

David Kessler, who as FDA commissioner first tackled the tobacco issue in the early 1990s, recalled the day he asked Zeller to become the point man for that undertaking.

“I said, ‘I need you for two weeks to work on tobacco, then you can go back to doing what you were doing,’ ” Kessler said. “Those two weeks turned into two years, turned into two decades. . . . Mitch cares deeply about this issue.”

So deeply, in fact, that he once proclaimed, “After my family, tobacco control is my first love.

Now, as Zeller returns as director of the FDA’s Center for Tobacco Products, created by Congress three years ago to regulate tobacco for the first time, there won’t be much space on his schedule for welcome parties.

The agency this year is expected to make a long-awaited decision on whether to ban menthol cigarettes, which studies show have boosted the number of smokers — particularly among African Americans, teens and low-income people — and make it harder to quit.

It faces pressure from public health advocates and industry officials over the backlog of 3,500 applications that tobacco companies have submitted for new products and changes to existing ones. Regulators have yet to rule on any of them, citing “significant deficiencies” in many applications.

At the same time, the center is assembling what will become a multi-year, multimillion-dollar anti-smoking campaign, targeted at young people and at-risk demographic groups such as African Americans, Native Americans and Hispanics.

There are ongoing legal battles with the industry over whether the FDA can force cigarette makers to put graphic warning labels on packages that show the consequences of smoking — such as images of a man exhaling smoke through a tracheotomy hole and a picture of cancer-ridden lungs.

In addition, the center faces an April 1 deadline to update Congress on the range of its efforts to rein in the tobacco industry. It also has said it will soon assert its authority to regulate a broader range of products, including cigars, pipe tobacco and electronic cigarettes.

On nearly every front, Zeller will face impatience from all directions.

Tobacco companies — unaccustomed to federal oversight, wary of restrictions that could shrink their bottom lines and willing to wage legal battles — have maintained at best a tense relationship with their new regulator and have looked for ways around existing regulations.

The waiting game over product applications encapsulates that uneasy relationship. FDA officials have said they are taking extra care in determining how best to evaluate products that have proved to be addictive and deadly. Tobacco companies such as industry giant Lorillard and others have argued that most of the changes are minor and insignificant and question why an office with 420 employees and a $505 million budget — funded by the industry — has refused to act.

“As a general rule, there has been no substantive response at all” to the applications, said Richmond attorney Bryan Haynes, whose firm Troutman Sanders represents multiple tobacco firms. “That presents a serious operational concern. . . . It’s absolutely stifling innovation.”

Tobacco control advocates and anti-smoking activists would like such “innovation” stifled indefinitely, particularly if it would lead to increased tobacco sales. They are eager for the new center to prove itself as a forceful regulator and to more rapidly use its powers to curtail smoking, the leading preventable cause of death in the United States.

“So far, they’ve been pretty toothless,” said Stanton Glantz, director of the Center for Tobacco Control Research and Education at the University of California at San Francisco.

Glantz praised the FDA tobacco center’s inaugural director, Lawrence Deyton, who is leaving for a post at George Washington University’s School of Medicine, for assembling a smart team of experts and laying the groundwork for meaningful regulation. He also said he has high hopes for Zeller. But he said he worries that the FDA, which is not allowed to ban nicotine or cigarettes outright, has been too willing to accommodate the concerns of the industry.

“The tobacco companies are not stakeholders,” Glantz said. “They are the opposition.”

Zeller, who could not be reached for comment, has shown impatience in the past. In an article last year in the journal Tobacco Control, he wrote that “action is sometimes sacrificed to process” at the FDA and that leaders there must instill a sense of urgency.

Tobacco industry representatives have reacted to Zeller’s appointment with skepticism.

“Somebody from a tobacco control background, you want to understand whether they’re going to regulate the industry in a reasonable way or not,” Haynes said.

Meanwhile, tobacco control advocates have welcomed Zeller with open arms, not only because of his decades-long history of fighting alongside them, but also because of his experience navigating the massive FDA bureaucracy.

“He understands the agency. He’s absolutely dedicated to using the agency’s authority aggressively. He’s knowledgeable about tobacco products and tobacco marketing, and he’s well-respected in the public health community,” said Matthew Myers, president of the Campaign for Tobacco-Free Kids, adding, “[He] has an opportunity to bring about important and fundamental change.”