Two years ago, investors were very excited about the future prospects of Jack in the Box (NASDAQ:JACK). At the 2012 Value Investing Conference, analyst Ryan Fusaro argued that Jack in the Box's Qdoba burrito brand could help the stock jump to $57 by 2015 -- at the time, it was trading at $27.50. Today, Jack in the Box is trading near $61, and Fusaro's dream has largely come true.

However, the company is still chasing the kind of success that Chipotle Mexican Grill (NYSE:CMG) has had. Chipotle increased comparable sales by 17.3% in its latest quarter, while Qdoba hit just 7.5% in its quarter. Qdoba is still streamlining, though, and there may be more growth ahead for the brand as it continues to focus on its stronger markets.

The Queso Burrito Fbff

Source: Qdoba.

Qdoba shuts stores, opens stores
In Jack in the Box's most recently reported quarter, the business closed down 62 Qdoba locations. Those were part of the brand's realignment, wherein it exited weaker markets in order to load up on winners. Along with openings in the quarter, the company ended the period with 632 Qdoba locations (up from 592 a year earlier). Compare that to the 1,681 locations Chipotle is managing, and it's clear Qdoba is still the up-and-comer.

Qdoba believes it can achieve Chipotle's scale, as well. The long-term plan is to operate 2,000 locations across America. In 2012, analyst Fusaro predicted the brand would be operating around 1,000 locations in 2015. That now looks optimistic, as Jack in the Box is only planning to open 60 in the next fiscal year, putting the grand total closer to 700.

That's good news for investors, though, as Qdoba and Jack in the Box have been able to push their success beyond Fusaro's prediction with even fewer resources. The smaller footprint also means Qdoba can make changes in its product line and operations more quickly than it could if it were larger.

The value of expertise
Much of Chipotle's high valuation -- it currently trades at a trailing price-to-earnings ratio of 60 -- comes from the business's high operating margin. Chipotle has a winning combination of a strong brand and efficient operations. The company's restaurant-level operating margin was 27.3% last quarter, while Qdoba's was 20.6%. 

That's more good news for Qdoba fans, as the company has some room to potentially grow into a stronger margin. While this quarter the brand took a hit from commodity costs, it saw less impact from discounting. That bodes well for the future as it reflects higher demand for the brand.

If Qdoba had hit Chipotle's operating margin, it would have earned an additional $5.7 million last quarter, representing an additional $3.7 million in after-tax earnings. Jack in the Box is theoretically sitting on an additional 15% increase in its quarterly earnings per share, if it can get its operations as tight as Chipotle's.

The bottom line
That doesn't mean the company will ever be able to do that. It may be that a 20.6% margin is as good as Qdoba can ever achieve, and that it only ever builds 1,000 or even 1,500 locations. Even so, the business is currently trading at a P/E of 29.2, making it significantly cheaper than Chipotle.

If Qdoba can unlock some of the potential in its income statement, it has a chance to seriously reward investors over the next few years. That doesn't even account for the other changes Jack in the Box can make to its name-brand operations, or the possibility that it could spin Qdoba off at some point. All of the upside makes it hard to ignore Jack in the Box, even if Chipotle is still sitting on the fast-casual throne.

Andrew Marder has no position in any stocks mentioned. The Motley Fool recommends and owns shares of Chipotle Mexican Grill. Try any of our Foolish newsletter services free for 30 days. We Fools may not all hold the same opinions, but we all believe that considering a diverse range of insights makes us better investors. The Motley Fool has a disclosure policy.