And yet, in three years, he has won a remarkable number of fans in the upper echelons of the book world. Most publishers in New York can’t say enough good things about him: smart, creative, tech-savvy — the list goes on. It helps that he has forged the friendliest relations between publishers and Barnes & Noble in recent memory. They are, after all, in this together.

Mr. Lynch grew up in Dallas and still speaks with a hint of Texas twang. But he has the foot-tapping intensity of a tech type running on four Mountain Dews. It seems fitting, then, that he usually works out of an office in the Chelsea neighborhood of Manhattan, where Barnes & Noble’s Web and digital operations are based, rather than at the company’s stately headquarters on Fifth Avenue, not far away. When he talks, you get the sense that he could be selling just about anything. As it happens, he is selling books.

Mr. Lynch says Barnes & Noble stores will endure. The idea that devices like the Nook, Kindle and Apple iPad will make bookstores obsolete is nonsense, he says.

“Our stores are not going anywhere,” he said in an interview this month in his office. He pointed to a surprisingly robust holiday season. In the nine weeks leading up to Christmas, sales were up 4 percent from the previous year. Titles for children and young adults are doing well, partly a result of the popularity of fiction with paranormal or dystopian themes, like “The Hunger Games.” And in the second half of 2011, Barnes & Noble picked up a big chunk of business from its vanquished rival, Borders.

Yet no sooner had the holidays passed than Barnes & Noble came out with some downbeat news for the year ahead. On Jan. 5, it projected it would lose as much as $1.40 a share in fiscal 2012. On top of that, Mr. Lynch said shareholders seemed to be underestimating the Nook’s potential so much that perhaps the company would be better off if it just spun off its digital business. Wall Street howled, and Barnes & Noble’s stock still hasn’t fully recovered. A bit of good news for the company is that, thanks to the Nook, it’s been grabbing e-book business from Amazon. Mr. Lynch said Barnes & Noble now held about 27 percent of the market, a number that publishers confirm gleefully. Amazon has at least 60 percent.

Responding to questions about the battle over e-books, Amazon issued a statement on Friday pointing to its own recent growth. In the nine-week holiday period ended Dec. 31, it said, “Kindle unit sales, including both the Kindle Fire and e-reader devices, increased 177 percent over the same period last year.”

Granted, Mr. Lynch inherited a company at a pivotal moment in its long, winding history. Barnes & Noble dates back to 1873, when Charles Barnes went into the used-book business in Wheaton, Ill. His company later moved to New York, bought an interest in an established textbook wholesaler, Noble & Noble, and opened a large bookshop on Fifth Avenue.