
This saying has its origin in an 18th century hymn written by William Cowper of England. This is the first three stanzas of that hymn.
God moves in a mysterious way
His wonders to perform;
He plants His footsteps in the sea
And rides upon the storm.
Deep in unfathomable mines
Of never failing skill
He treasures up His bright designs
And works His sovereign will.
Ye fearful saints, fresh courage take;
The clouds ye so much dread
Are big with mercy and shall break
In blessings on your head.
The hymn was inspired by what Jesus said in:
John 13:7 (NLT)7 Jesus replied, “You don’t understand now what I am doing, but someday you will.”
There is nothing wrong with the words of this hymn. God does work in ways that we don’t understand and that are mysterious to us. God’s ways don’t conform to our human motives or reasoning.
Isaiah 55:8 (NLT)8 “My thoughts are nothing like your thoughts,” says the LORD. “And my ways are far beyond anything you could imagine.
The point is that this saying, “God works in mysterious ways”, is not in the Bible. It is often quoted as praise after God has done something that can’t be explained, or it may be just an expression in difficult times and we want to blame God. As I have written in other posts, Hod allows tough times He doesn’t cause them. Some of those times are the result of the actions and activity of Satan and his forces, others the result of things we do or don’t do, or the mear fact that we live in a fallen world (Take Responsibility, Stop Blaming The Devil And Use The Power And Authority That You Have In Christ, Does God Test Christians? ) Sometimes we use this saying as an excuse for not wanting to know or understand God. After all He’s so mysterious there is no way to know him right? Well, there is a scripture that completely debunks that idea.
We can know God but we can never really comprehend everything about Him.
Isaiah 55:6 (NLT)6 Seek the LORD while you can find him. Call on him now while he is near.
While God reveals a great deal about Himself in Scripture and through the Holy Spirit, we can know God we can never comprehend everything about Him.
John 16:13 (NKJV)13 However, when He, the Spirit of truth, has come, He will guide you into all truth; for He will not speak on His own authority, but whatever He hears He will speak; and He will tell you things to come.
We don’t have the capacity fully to understand all of His greatness and glory.
Romans 11:33-36 (NLT)33 Oh, how great are God’s riches and wisdom and knowledge! How impossible it is for us to understand his decisions and his ways!34 For who can know the LORD’s thoughts? Who knows enough to give him advice?35 And who has given him so much that he needs to pay it back?36 For everything comes from him and exists by his power and is intended for his glory. All glory to him forever! Amen.
God does things that are beyond our limited experience and ability to comprehend.
Romans 11:33-35 (NKJV)33 Oh, the depth of the riches both of the wisdom and knowledge of God! How unsearchable are His judgments and His ways past finding out! 34 "For who has known the mind of the LORD? Or who has become His counselor?"35 "Or who has first given to Him And it shall be repaid to him?"
Deuteronomy 29:29 (NKJV)29 The secret things belong to the LORD our God, but those things which are revealed belong to us and to our children forever, that we may do all the words of this law.
We don’t know why He allows certain things to happen to us but we know that whatever happens He will never leave or forsake us.
Deuteronomy 31:6 (NLT)6 So be strong and courageous! Do not be afraid and do not panic before them. For the LORD your God will personally go ahead of you. He will neither fail you nor abandon you.”
God’s methods often leave us completely confused. Why would He tell Joshua and the children of Israel to march around the city of Jericho for a week?
Joshua 6:1-4 (NKJV)1 Now Jericho was securely shut up because of the children of Israel; none went out, and none came in.2 And the LORD said to Joshua: "See! I have given Jericho into your hand, its king, and the mighty men of valor.3 You shall march around the city, all you men of war; you shall go all around the city once. This you shall do six days.4 And seven priests shall bear seven trumpets of rams' horns before the ark. But the seventh day you shall march around the city seven times, and the priests shall blow the trumpets.
What purpose would it serve for a young girl to after diving into shallow water break her neck on a submerged rock and then spend the rest of her life in a wheelchair? That young woman is Joni Eareckson Tada. This is she wrote in her book “A Step Further” in response to letter she received from a young man that had been in an accident who was bitter at God for allowing him to suffer.
“If God decided to explain all His ways to me, what makes me think I would be able to understand them? It would be like pouring million-gallon truths into my one-once brain. Didn’t one Old Testament author write, ‘As you do not know the path of the wind, or how the body is formed in a mother’s womb, so you cannot understand the work of God, the Maker of all things’ (Ecclesiastes 11:5)? In fact, the whole book of Ecclesiastes was written to convince people like me that only God holds the keys to unlocking the mysteries of life and that He’s not loaning them all out! If God’s mind was small enough for me to understand, He wouldn't be God! Yet, in spite of this, He has chosen to have a personal relationship with me - that’s the greatest mystery of all!” (p. 173)
John 3:16 (NKJV)16 For God so loved the world that He gave His only begotten Son, that whoever believes in Him should not perish but have everlasting life.
1 John 4:8-10 (NKJV)8 He who does not love does not know God, for God is love.9 In this the love of God was manifested toward us, that God has sent His only begotten Son into the world, that we might live through Him.10 In this is love, not that we loved God, but that He loved us and sent His Son to be the propitiation for our sins.
He keeps every promise that He makes.
Deuteronomy 7:9 (NLT)9 Understand, therefore, that the LORD your God is indeed God. He is the faithful God who keeps his covenant for a thousand generations and lavishes his unfailing love on those who love him and obey his commands.

While God works in ways we don’t understand, ways that are mysterious to us, He has revealed His greatest mystery.. What’s the mystery? The mystery is that Christ, came to dwell in all people. Not just the Jewish people but all people.
Colossians 1:26-27 (NKJV)26 the mystery which has been hidden from ages and from generations, but now has been revealed to His saints.27 To them God willed to make known what are the riches of the glory of this mystery among the Gentiles: which is Christ in you, the hope of glory.
Today we We Christians take God's blessing for granted. But for the Gentile believers, that Paul was writing to in Colossae, to realize that the Messiah came for them too, was a tremendous revelation.
If Christ is in us then the focus is not on us anymore but on Christ.
Galatians 2:20 (NKJV)20 I have been crucified with Christ; it is no longer I who live, but Christ lives in me; and the life which I now live in the flesh I live by faith in the Son of God, who loved me and gave Himself for me.
2 Corinthians 3:18 (NKJV)18 But we all, with unveiled face, beholding as in a mirror the glory of the Lord, are being transformed into the same image from glory to glory, just as by the Spirit of the Lord.
Though we may not understand everything that God does about where we fit into God’s plan we know that whatever happens works to our benefit.
Romans 8:28-29 (NKJV)28 And we know that all things work together for good to those who love God, to those who are the called according to His purpose.29 For whom He foreknew, He also predestined to be conformed to the image of His Son, that He might be the firstborn among many brethren.
Yes, the Bible makes it perfectly clear that God does move in mysterious ways, although the saying is not there. However He has revealed His greatest mystery, “Christ in you”. If you haven’t received Jesus into your heart please consider it not. Only then can you understand the mystery of Christ in you and yes that’s in the Bible. That’s the one truth that makes all the difference.