Supermarket chain Whole Foods Market (WFM) is an excellent investment opportunity for those who already own Sprouts Farmers Market(SFM) - Get Report , or for those looking to get into the health grocery store chain.

The year-to-date (YTD) performance metrics for both these stocks tell you their true potential; while Sprouts Farmers Market is down 6.3% YTD, Whole Foods Market, riding high on analyst upgrades and the new 365 format potential, is on an upward trajectory and affords long-term growth. A battle royale between these two heavyweights was a long time coming.

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Whole Foods Market is the largest retailer of natural and organic foods and is also the first certified organic grocer in the United States.

On the other hand, Sprouts Farmers Market through its subsidiaries operates as a specialty retailer of natural and organic food. Both are consumer-defensive stocks.

While smaller company Sprouts has been able to grow sales by a much faster clip from 2010 compared to Whole Foods, in terms of profit margins both companies look the same with 3%-to-4% margins.

The bullish case for Whole Foods Market is its larger size, greater free cash flow and lower beta (i.e. stock volatility).

Against Sprouts Farmers' $3.7 billion in sales, Whole Foods is nearly four-fold bigger with $15.59 billion in sales. Currently, it has 446 stores in the United States, Canada, and the United Kingdom. Sprouts Farmers' operates more than 230 stores in thirteen states from coast to coast.

Now everybody knows that the grocery chain business is all about volumes and Whole Foods is a far better value proposition. With Whole Foods Market debuting its 365 grocery chains, we believe it has outperformed peers like Sprouts Farmers and United Natural Foods via the small-format 365-day-a-year store aimed at urban millennials shopping a lower price points.

This leverages Whole Foods in the beginning of a market transposition that could set it up for victory in the long term. Credit Suisseagrees.

As we've often mentioned, Free Cash Flow is a superb metric to assess the real cash a company generates. Unlike many on Wall Street who focus myopically on earnings (SFM is projected to offer faster EPS growth than WFM), it's important to understand that earnings numbers can be manicured by slick moves, but cash flow is much tougher to manufacture.

With a FCF of about $100 million a year, Sprouts Farmers Market is not as attractive as Whole Foods Market, which delivers nearly 8 times that FCF ($791 million) despite being five times the size of Sprouts Farmers in terms of annual revenues.

On a price-to-cash flow basis, WFM at 11.8 times trades at a surprising discount to SFM which sports a 21.7 times P/E. This is indicative of the value Whole Foods Market as an investment can offer.

While its peer Kroger may appear to be best positioned to handle competitive pressures from non-traditional grocers, look at WFM because of the hefty buybacks ($1 billion in shares). Friendly shareholder policies like these, add more zing to owning WFM.

Whole Foods Market stock has a lower beta (0.82), best suited for investors not comfortable with huge price swings. Sprouts Farmers Market, despite scoring over WFM in some cases, is a highly volatile stock with a beta of above 4, making it prone to roller-coaster rides.

Buy WFM for stable earnings, new growth opportunities and a stronger cash war chest.

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This article is commentary by an independent contributor. At the time of publication, the author held no positions in the stocks mentioned.