(FORTUNE Small Business) – You'd think Satan himself had come marauding into town. There I was, chatting Scripture with Bible-belting entrepreneur S. Truett Cathy, when my time with him was nearly cut short by the forces of flakdom. Donald A. Perry, vice president of public relations at Chick-fil-A, the $1.2 billion chicken restaurant chain Cathy founded in 1967, kept trying to bring the discussion to a halt. "What would you like to do?" he finally interrupted me to say. "Are you going to continue on a religious kind of thing, or are you going to concentrate more on the Chick-fil-A business?" He helpfully suggested that I might want to set "some ground rules" with Cathy if "you really want to probe more philosophical, biblical kinds of things." Cathy, who is 81, gently put a stop to our ungodly bickering. "I'm comfortable continuing on this," he intoned, signaling me to go on.

That conflict is what makes the company, which is based in Atlanta, so intriguing. Cathy's handlers try to present him as a man of deep religious conviction who also runs a nationwide fast-food empire. But the two facts are more intertwined than that. Last summer, testifying before a House subcommittee on business ethics, he talked openly about "incorporating biblical principles into business." It sounds like the sort of proposition that even the most ardent deity doubter could support, especially in an era in which so many CEOs have confessed to being crass and self-centered. Could religion provide their ilk with the kind of valuable wisdom and meaningful direction they sorely need? Indubitably.

Nevertheless, at Chick-fil-A, the corporate commandments can seem overbearing. Look inside the company, and it's clear that Cathy himself draws no line between his Christian beliefs and his capitalistic instincts. All 1,100 or so Chick-fil-A units are required to close on what Cathy labels the "Lord's day." (Note to the lapsed: That's Sunday.) No use trying to talk him out of it, he says, because it's his company and that's what he wants to do. The founder's answer to operators who celebrate the Sabbath on another day: Hey, do what you want, but you can close the restaurant only on Sunday. That could make some non-Christians feel unwelcome. Indeed, one former employee has recently filed suit, claiming he was fired for not being Christian.

Cathy gets points for his candor, if not his sensitivity. When asked about people who follow other faiths, he simply responds, "God will judge." Nobody enters headquarters credibly thinking, as Genesis puts it so well (28:16), "Surely the Lord is in this place; and I did not know it!" A plaque outside lists Chick-fil-A's corporate purposes, the first being "to glorify God by being a faithful steward to all that is entrusted to us." And if such words make an individual uncomfortable? "That's up to that person as to whether he felt comfortable or not," replies Cathy. "If he didn't, he wouldn't come in. He can sit on the outside."

As long as he's alive--and he has plans to make it to Strom Thurmond territory--Cathy won't gloss over Chick-fil-A's core belief system with a euphemistic "holiday party." No, he'll continue throwing his "Christmas open house," replete with live reindeer. Dan Cathy, Truett's 49-year-old son and the company's president and chief operating officer, has no trouble explaining that Chick-fil-A schedules "blatantly Christian worship" during its annual meeting for operators. But "we make sure there's another activity scheduled at that time," says Dan, who is fond of words like "dad-gum." "We want people to know they have a choice." The same can be said about the weekly devotional meeting, held at headquarters every Monday morning at 8:30. Only about a third of the nearly 500 employees who work there typically show up--not that anyone takes attendance exactly. "I don't know where the other two-thirds are, but they've still got very responsible jobs here," Dan points out. And he can't remember ever hearing any grousing from anyone about the company's management style. "I'm sure there might be some people who have a negative response to what we do, but I don't think they would express that to me," he says.

In October one terminated employee expressed such sentiments via court papers. The former employee, Aziz Latif, claims that he was training to become a franchise operator in November 2000 when he was fired because of his Muslim faith. According to Ajay Choudhary, his Houston-based lawyer, Latif says he lost his job "one day after he did not participate in a prayer to Jesus Christ." Choudhary notes that Latif, who started working at Chick-fil-A in 1994--which suggests that he felt okay about the place for six years--"received excellent performance evaluations, including one the week he was fired." Chick-fil-A, adds Choudhary, "is a Christian company, and it takes religion very seriously. Religion should not be brought into the workplace. What does glorifying God have to do with making chicken?"

Truett Cathy's response: "He was not fired on account of that. He wasn't required to pray; he had the choice to pray. We don't force our religion on anybody." Dan goes so far as to label the suit "frivolous" and doesn't expect it to change anything. A couple of years ago he even signed a contract he had drafted promising his parents that he'd manage the company just the way his dad does. "I don't feel the need to leave my mark" by changing the company's policies, he says. In other words, he agrees with what Truett told me: "I see no conflict between biblical principles and good business practices. You don't have to be a Christian to work at Chick-fil-A, but we would ask you to base your decisions on biblical principles because no one could argue with that."

That's not as straightforward as it sounds--as I pointed out to Cathy, only to provoke Perry's scolding. By that standard employees who are known to be homosexuals "shall surely be put to death," as it sayeth in Leviticus (20:13). Cathy conceded that he wouldn't be adopting that particular principle. "I'm not a Bible scholar--I'll tell you that," he added humbly.

He isn't, and that's what is appealing about him. Cathy presents himself as an utterly fallible human being. Read his book, which carries the somewhat hokey title Eat Mor Chikin: Inspire More People ($20; available wherever better Bibles are sold), and he comes across often as unsure and as inconsistent as the rest of us. "I prefer to seek His counsel on issues more vital than the day-to-day operations of the company," he writes of his relationship with God. Eighteen pages later, facing a severe business downturn, he cries out to God for help.

He's hardly unaware of his own contradictions. Cathy admits that he can't forgive his father for never saying that he loved him. "That's not biblical of me," he concedes. "I think I should." He's just doing his best to make sense of a life that has included unimaginable tragedy (his brothers died in a plane crash) and wild success in business. Cathy's main fault, as filtered through his management style, is that he thinks he knows better than everyone else. But then again, try to find me an entrepreneur who doesn't.

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