Whole Foods Market posted third-quarter earnings on Wednesday that beat analyst expectations.

EPS: 36 cents adjusted vs. 33 cents expected, according to Thomson Reuters

Revenue: $3.73 billion vs. $3.72 billion expected, according to Thomson Reuters

U.S. same-store sales: down 1.9 percent vs. down 2.2 percent expected, according to StreetAccount

In the third quarter, net income fell to $106 million, or 33 cents per shares, from $120 million, or 37 cents a share, a year ago.

However, on an adjusted basis, Whole Foods earned 36 cents per share, ahead of the 33 cents per share projected by a Thomson Reuters survey.

Revenue of $3.73 billion a touch higher than Wall Street's estimate of $3.72 billion.

In addition, the company said its same-store sales fell 1.9 percent in the quarter, a narrower than expected decline. Wall Street estimated that Whole Foods same-store sales would fall 2.2 percent in the quarter, according to StreetAccount.

"Our comparable store sales improved sequentially on a one- and two-year basis in the third quarter, and that momentum has accelerated 220 basis points in the fourth quarter, resulting in positive overall comps for the first three weeks," John Mackey, co-founder and CEO, said in a statement Wednesday.

Whole Foods declined to comment further on the results to CNBC. Due to the pending acquisition, the company will not be holding a conference call with analysts.

Whole Foods made headlines last month after tech retailer Amazon agreed to buy the grocery store chain for $42 a share, in a deal valued at $13.7 billion. The company said that the deal is on track to close during the second half of 2017.

Whole Foods was under pressure from activist investor Jana Partners, which had called on Whole Foods to sell itself. The investor had criticized Whole Foods for its poor performance and suggested the chain could be merged with another grocer.

Jana has since cashed out of its stake, making a profit of roughly $300 million.

When the deal was announced, it sparked a selloff of grocery store stocks, as investors expect Amazon to put more pressure on prices in the already competitive sector.

With the acquisition of Whole Foods, Amazon quickly gains a network of physical stores, which can aid it in distributing products to customers. While few people purchase their groceries online right now, more shoppers are switching to purchase goods that way.

Millennials, in particular, are leaning toward ordering their groceries online. Older millennials, over age 25, were twice as likely to buy online. This generation is starting to get married and have children and will be growing their grocery spend over the next decade.

In the third quarter, Whole Foods opened six stores, including one relocation. In the fourth quarter, the company opened two stores, and expects to add two additional Whole Foods Market stores and two Whole Foods Market 365 stores, including one relocation.

Mackey will remain CEO of the grocery store chain after the deal closes, and the store will continue to operate under the Whole Foods brand.

"This partnership presents an opportunity to maximize value for Whole Foods Market's shareholders, while at the same time extending our mission and bringing the highest quality, experience, convenience and innovation to our customers," Mackey said of the deal last month.