“As sure as God made little green apples” means extremely sure. The ssaying “as sure as God made apples” has been cited in print since at least 1828, “the good Lord made green apples” has been cited in print since at least 1895 and “sure as somebody made little green apples” has been cited since at least 1904. “Little green apples” has become the more popular form of the phrase.
 
The author of the saying is not known and it’s also not known why “green apples” is used, but apples were very popular in the United States in the 19th century, far ahead of all other fruits. Also, the apple was believed by many at the time to have been the forbidden fruit (some scholars claim the fruit was a quince) specified in the biblical story of Adam and Eve in the Garden of Eden.
   
 
Idioms Glossary
as sure as God made little green apples
Definition: Something is an absolute certainty.
Explanation: A Christian with lots of faith has no doubt at all that God made little green apples and everything else on earth.
       
Google Books
Sayings and Doings; Or Sketches from Life
Third Series
Vol. III
London: Henry Coburn
1828
Pg. 291:
“Mr. F., as sure as God made apples,” cried the terrified Thespian.
 
25 July 1875, Chicago (IL) Daily Tribune, “Old Uncle Billy,” pg. 7:
That’s as sure as God made apples.
   
Google Books
Harold Saxon:
A story of the church and the world
By Alan Muir
London: Smith, Elder, & Co.
1880
Pg. 136:
“True as God made apples,” Tabitha Eve replied.
   
Google Books
The True Story of St. Paul’s Industrial School,
as told by its young inmates, their parents and friends
Edited by Elizabeth Surr
London: Blades, East & Blades
1882
Pg. 8:
He says, all is true “as God made apples.”
 
5 June 1895, Hamilton (OH) Daily Republican, “One Doctor Bundy,” pg. 3, col. 2:
If Peter had said a word Joe would have jumped him as sure as the good Lord made green apples.
 
5 December 1903, Oregonian (Portland, OR), pg. 11:
The Willamette Valley Association will carrry over a large stock, just as sure as God made green apples.
 
Chronicling America
4 December 1904, New York (NY) Daily Tribune, “Miss Harding’s Last Game” by Frederick Upton Adams, Sunday Magazine, pg. 12, col. 1:
“Let that ball alone, you slab-sided, broken-horned derelict! She’s got it, Carter, and she’ll swallow it sure as somebody made little green apples.”
 
2 March 1907, Warsaw (IN) Daily Union, “Too Quick in Action,” pg. 10, cols. 1-2:
He was wide open all right, and there was a big delivery wagon unloading stuff in the back end of his warehouse, and as sure as the Lord made little green apples that wagon was from Brown & Co.—firm I’m with, you know.
 
Chronicling America
5 September 1912, Mathews Journal (Mathews Court House, VA), pg. 3, col. 6:
The Lord made little green apples, but the Lord knows who made little boys to eat them.—Alexandria Gazette.
 
Google Books
October 1916, The Green Book Magazine, “As the Cat Jumps” by William Harper Dean,  pg. 691:
“He’ll maul the kid sure’s God made little green apples!”
 
3 September 1920, Kansas City (MO) Star, “The Killer” by Stewart Edward White, pg. 29:
Or rather, bless him; for as I just said, if he had not tolled away our mounted pursuit we would have been caught as sure as God made little green apples.
 
OCLC WorldCat record
God made little green apples
Author: Frank Elliott
Publisher: Boone, N.C. : DML Productions, 1977.
Edition/Format:  Book : Fiction : English