“That’s the way the cookie crumbles” (also “that’s how the cookie crumbles”) means that even a good thing (a cookie) sometimes breaks apart. A similar expression accounting for unfortunate events is “That’s life!”
 
William E. (“Bill”) Vaughan (1915-1977) wrote in his “Starbeams” column in the Kansas City (MO) Star on February 22, 1955:
 
“The teen age lovely down the street reports that her father is unbearably square. To express a certain fatalism he still says, ‘That’s the way the ball bounces’ instead of ‘That’s the way the cookie crumbles.’”
 
It’s uncertain if Vaughan coined the expression or just popularized it from teenage slang that he’d heard. “Well, that’s when the cookie crumbled, right there” was published in the Long Beach (CA) Independent on August 24, 1956.
 
The “cookie” expression is dated and is infrequently used today.
 
[This entry was assisted by subsequent research by Word Histories.]
   
 
The Free Dictionary
That’s the way the cookie crumbles. (British, American & Australian, informal, American, informal)
something that you say which means that bad things sometimes happen and there is nothing you can do to prevent it, so it is not worth becoming upset about it.
I can’t believe they chose Sam for the job and not me. Ah well, that’s the way the cookie crumbles.
   
(Oxford English Dictionary)
cookie
Colloq. phr. (chiefly U.S.): (that’s) how (or the way) the cookie crumbles, (that is) how the position resolves itself; that is the way it is.
1957 Sat. Even. Post 7 Sept. 59 From then on, that’s the way the cooky crumbled. I enjoyed having good ratings, but I didn’t enjoy the viciousness of the railbirds’ thrusts at Berle.
1959 WENZELL BROWN Cry Kill iv. 45 No matter how the cookie crumbled, Mamma Ida was in for a bad time.
1961 WODEHOUSE Ice in Bedroom v. 40 Oh well, that’s the way the cookie crumbles. You can’t win ‘em all.
1964 Listener 16 Apr. 612/2 We shall not know how, as the Americans say, the cookie crumbles.
 
Wikipedia: William E. Vaughan
William E. (“Bill”) Vaughan (October 8, 1915 – February 25, 1977) was an American columnist and author. Born in Saint Louis, Missouri, he wrote a syndicated column for the Kansas City Star from 1946 until his death in 1977. He was published in Reader’s Digest and Better Homes and Gardens under the pseudonym Burton Hillis. He attended Washington University in St. Louis.
 
His folksy aphorisms (published in his “Starbeams” feature) are often collected in books and on Internet sites
   
22 February 1955, Kansas City (MO) Star, “Starbeams,” pg. 26, col.
The teen age lovely down the street reports that her father is unbearably square. To express a certain fatalism he still says, “That’s the way the ball bounces” instead of “That’s the way the cookie crumbles.”
(Bill Vaughan is credited after the last item.—ed.)
 
23 February 1955, The Enquirer (Cincinnati, OH), “Innocent Bystander” by Ollie M. James, pg. 4, col. 7:
Well, as we say in the publishing business, sometimes that is the way the cookie crumbles.
   
28 February 1955, Muncie (IN) Star, “Senator Soaper Says” by Bill Vaughan, pg. 4, col. 4:
The teen-age lovely down the street reports that her father is unbearably square. To express a certain fatalism he still says, “That’s the way the ball bounces” instead of “That’s the way the cookie crumbles.”
 
3 March 1955, Uniontown (PA) Evening Standard, “The Junior Reporter Club,” pg. 27, col. 2:
Well that’s the way the cookie crumbles.
 
27 November 1955, Helena (MT) Independent Record, “Freckles and His Friends” comic, pg. 47:
SORRY, DAD, BUT THAT’S THE WAY THE COOKIE CRUMBLES.
 
29 March 1956, Mexia (TX) Daily News, pg. 10, col. 1:
“Oh well, that’s how the cookie crumbles.”
 
13 August 1956, Portsmouth (OH) Times, pg. 22, col. 1:
THAT’S THE WAY the cookie crumbles.
 
24 August 1956, Long Beach (CA) Independent, pg. 2, col. 1:
WELL, THAT’S when the cookie crumbled, right there.
 
10 October 1958, New York (NY) Times, pg. 38:
“But,” he said, using a common among baseball players, “that’s the way the cookie crumbles and that’s the way the ball bounces.”
   
5 March 1959, Washington (DC) Post, “Cookie Record Crumbles,” pg. C11:
“THAT’S the way the cookie crumbles”—a slang phrase favored by teen-agers—has special meaning for a pair of Fairfax County Girl Scouts.
 
Google Books
The Zoo Story: The Death of Bessie Smith; The Sandbox; Three Plays
By Edward Albee
New York, NY: Coward-McCann
1960
Pg. 18:
JERRY (Lightly mocking) But that’s the way the cookie crumbles?