CNBC's Jim Cramer suggested investors take advantage of Tuesday's relief rally to protect stocks gains as coronavirus fears linger. The "Mad Money" host explained why short-sellers are giving the market some extra boost after Friday's sell-off. Later in the show, he sat down with Chipotle CFO Jack Hartung to get an update on the company's new loyalty program and digital strategy.

CNBC's warned Tuesday that investors should not turn bullish in the midst of a relief rally on Wall Street and take the time to do some profit-taking.

"Today seemed like a genuine relief rally, meaning it was motivated by a sense of relief that we'll make it through the epidemic intact, or at least in much better shape than we thought a few days ago," the "Mad Money" host said. "But let's not get ahead of ourselves — to me, this is an opportunity to do some portfolio reshuffling."

The stock market is rallying, and short sellers who reacted to last week's declines are partly responsible for it, Cramer said.

"So much of today's rally took place on the backs of hedge funds who were poorly positioned going into the sell-off on Friday," the host said. "So they overcompensated by shorting anything related to the coronavirus right into the teeth of the downturn."

has registered 8.5 million members on its new loyalty program in less than a year and "we're just getting started," Chief Financial Officer Jack Hartung told Cramer.

"We think that's attributed to the natural loyalty that people have to the Chipotle brand, but also to the marketing and awareness building to, you know, attract people into the program," he said in the "Mad Money" interview. "The best thing though, Jim, is we haven't really monetized that. We haven't really turned that into a personalized program where we're communicating on a one-to-one basis with our customers."

In Cramer's lightning round, the "Mad Money" host ran through his thoughts about callers' favorite stock picks of the day.

: "I think we're late to the party. Now that said, it's down 3 today. If you want to get involved, at least you had to buy yesterday when they got the news, but I think we are late."

: "I think it's a good solid franchise. I'm not saying it's going to shoot the lights out. I think it's fine."

: "Look, we are a big believer in immunotherapy now that we have gene-sequencing, and that's part of the speculative box that we are in favor of."