Getting a job at Whole Foods Market can be a challenge. I know this because I now work in the recruiting side of things. I applied several times before finally attending a Job Fair for a new store opening. If you choose to go this route, be prepared for a long day and some disorganization, so bring your patience with you.
If you don't choose to go this route, and apply to work at a more established store, AND if you're lucky enough to get a call back, also bring your patience because it's a long process. First, you submit your application online. Luckily, you only have to create a profile once, but you can apply to as many positions as you want at any given time there are open positions. IF you get a call back, you will be asked several questions over the phone. Make sure you have done some research on the company first (i.e. read about their mission, Core Values, quality standards, non-profit organizations, etc.). It definitely helps to shop at WFM because they will likely ask you about what else you know about the store. If you phone interview well, they will ask you to either 1) come in for a Group Interview, or 2) come in for a one-on-one interview. The Group Interview is a fun, engaging way to interview, but does tend to celebrate and reward extroverts. If you're introverted, your chances will be better at a one-on-one interview. After that interview, you may be asked to go to a second interview on top of that.
If you finally get a job offer, then you have to have a couple more hoops to jump through to become an official Team Member, which includes surviving the probationary period, as well as a team voting process. It's very involved!!!