"It’s not the minutes at the table that make you fat—it’s the seconds” is a pun that plays upon the word “seconds” (meaning “second helpings” or “second servings"). The joke has been cited in print since at least 1956.

A similar pun on the word “seconds” is “Seconds count—especially when dieting.”


Google News Archive
1 September 1956, Charleston (SC) News and Courier, “Doing The Charleston With His Lordship” by Ashley Cooper, pg. 6A, col. 5:
DIGGING INTO the treasure trove of stolen jokes, Lord Ashley answers the questions:

Q. Do you think it is true that all fat people spend too much time at the dinner table? (Fat lady)
A. It’s not so much the minutes at the table. It’s the seconds.

31 May 1959, Aberdeen (SD) Daily News, “Earl Wilson’s New York,” pg. 4, col. 5:
“It’s not the minutes you put in at the dinner table that make you fat—it’s the seconds!”

25 June 1959, National Road Traveler (Cambridge City, IN), pg. 7, col. 4:
It isn’t the hours one spends at the table that put on the avoirdupois; it’s the seconds. 

Google Books
September 1960, Boys’ Life, “Think and Grin,” pg. 86, col. 2:
A little man talking to a fat Lady: It’s not the minutes you put in at the table that make you fat. It’s the seconds. — Robert Carroll, Garner, N.C.

5 December 1962, Springfield (MA) Union, “Today’s Chuckle,” pg. 1, col. 3:
It’s not the minutes you spend at the table that make you fat—it’s the seconds.

Google News Archive
26 December 1963, The Forum (Nucla, CO), pg. 1, col. 3:
Tip to weight watchers this holiday season...It’s not the minutes you spend at the table that makes you fat...it’s the seconds.

Google News Archive
19 November 1982, Wilmington (NC) Morning Star, “Over Your Coffee” by Miriam Gessner, pg. 7A, col. 1:
It’s not the minutes you spend at the table that make fat—it’s the seconds.

Google Books
20,000 Quips & Quotes
By Evan Esar
New York, NY: Barnes & Noble Books
1995, ©1968
Pg. 863:
It’s not the minutes you take at the table that add to your weight — it’s the seconds.