It doesn't. This quote comes from an old poem or hymn, but may be based on Isaiah 55:8-9.
Isaiah 55:8 "For my thoughts are not your thoughts, neither are your ways my ways," declares the LORD.
9 "As the heavens are higher than the earth, so are my ways higher than your ways and my thoughts than your thoughts.
The phrase, "God works in mysterious ways" is not found word-for-word...in fact, the word "mysterious" doesn't appear in the King James Bible at all.
This popular saying is actually a paraphrase based on verses that speak of Godly things as (previously) unknown, or "mysteries." Here are some pertinent passages that give rise to the saying:
Ecclesiastes 1:5 - As you do not know what is the way of the wind, Or how the bones grow in the womb of her who is with child, So you do not know the works of God who makes everything.
Jeremiah 33:3 - 'Call to Me, and I will answer you, and show you great and mighty things, which you do not know.'
Mark 4:11, 12 - And He said to them, "To you it has been given to know the mystery of the kingdom of God; but to those who are outside, all things come in parables, so that 'Seeing they may see and not perceive, And hearing they may hear and not understand; Lest they should turn, And their sins be forgiven them.' "
1 Corinthians 2:7 - But we speak the wisdom of God in a mystery, the hidden wisdom which God ordained before the ages for our glory,
Ephesians 3:9 - and to make all see what is the fellowship of the mystery, which from the beginning of the ages has been hidden in God who created all things through Jesus Christ;
1 Timothy 3:16a - And without controversy great is the mystery of godliness:
It should be noted that nearly every time the New Testament refers to a "mystery," it's in conjunction with something that was previously unknown being revealed or explained (Mark 4:11, above). This is one of the great purposes of the New Testament: in it, much of the "mystery" of God is revealed!
Colossians 2:2, 3 - that their hearts may be encouraged, being knit together in love, and attaining to all riches of the full assurance of understanding, to the knowledge of the mystery of God, both of the Father and of Christ, in whom are hidden all the treasures of wisdom and knowledge.
[Quotes from NKJV]
If you look in the New Living Translation Isaiah 45:15 says "Truly, O God of Israel, our Savior, you work in mysteriousways."
Another perspective:
There are many mentions or allusions to God doing things "in mysterious ways", which is often a substitute for events or situations for which mankind is unable to offer an explanation.
However, Paul actually makes a clear case that PRIOR to Jesus, there were a great many things that were unexplainable to humans, but that after Christ the true "mystery" was the church and it was now being revealed.
In John 14-17, Jesus several times states that the Holy Spirit was to come upon us and reveal all knowledge. One can infer from that this that, after that point, nothing would remain a mystery .
Final thought: It is easy for us to place the onus on God for things we do not understand, rather than take the time in prayer, study and meditation to seek Him for the answer. And sometimes what we ascribe to God working in mysterious ways is our own failure to listen to Him as he was trying to explain. The Word of God says that if anyone lack wisdom to ask. Wisdom removes the veil from mystery.
Sometimes you don't wanna believe, but never stop believing.
There is no specific scripture for this phrase. It comes from a hymn called "God Moves In a Mysterious Way".
God works in mysterious ways.....
The Devil Works in Mysterious Ways - 2011 was released on: USA: 23 February 2011 (Salt Lake City, Utah)
The cast of The Devil Works in Mysterious Ways - 2011 includes: Kami Coleman as Women Shaun Ford as Pawn Shop Clerk
William Cowper wrote a hymn called ' God Moves in a Mysterious Way'
No one can say as God works in mysterious ways.
shows how faith can get you through anything in life. God works in mysterious ways
In Mysterious Ways was created on 1985-09-23.
Mysterious Ways - 2009 was released on: USA: 2009
The duration of Mysterious Ways - TV series - is 3600.0 seconds.
Perhaps it is in the Bible, but by faith alone you know that God works in His time. The Hebrew people were God's chosen ones. They were filled with faith that God would one day free them. God works in mysterious ways no one can understand.
Mysterious Ways - TV series - was created on 2000-07-24.
In Mysterious Ways - 1914 was released on: USA: 16 January 1914