Exhibit 31.6

CERTIFICATIONS

I, Glenda Flanagan, certify that:

1.I have reviewed this Quarterly Report on Form 10-Q/A of Whole Foods Market, Inc.; and

2.Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report.

Date: August 10, 2012

/s/Glenda Flanagan

Glenda Flanagan

Chief Financial Officer