Where do doubts come from? In general, I think most doubts come when there is a disconnect between what we see or experience, and what we believe to be true. Doubt can be stubborn. It can cloud our judgment, cause us to be pessimistic, and steal our joy. Doubt makes us believe our presumptions of the truth were wrong.
Spiritual doubt for believers is something attune to a spiritual flu. It generally affects all of us from time to time. Sometimes it is severe, sometimes not so much. It can be short lived and it can drag on for a while. It can affect only parts of the body or it can make you hurt all over. Fortunately, God gives us a remedy for doubt.
In Luke 24, after Jesus resurrection, the women who went and found the empty tomb were telling the disciples about it. Luke records their response this way, "but these words seemed to them an idle tale, and they did not believe them." They doubted. Jesus had told them everything that would happen in the last week of His life while he was still alive, including His resurrection, but what they knew to be true about death blinded them to the reality of Jesus' resurrection. A few verses later, starting in verse 36, Jesus shows up in the midst of the disciples and says "Peace to you!." Well they were startled. They were still coming to grips with the reports of Jesus' resurrection and His sightings. They assumed they were seeing a spirit. Then Jesus ask them this question, a question he may be asking you today.
"Why are you troubled, and why do doubts arise in your hearts? - Jesus, Luke 24:38
Jesus offers the disciples three remedies for their doubts. First, He encourages them to examine Him, His hands and His feet. Basically saying, I am not a figment of your imagination. I bear the marks of the crucifixion and I am alive. He even encourages them to touch Him. We don't have that luxury today. However, He is as real today as He has always been, and we are encouraged to examine Him. We are encouraged to experience Him. We are to remember all that he has done for us through his crucifixion and the faithfulness we have experienced in our relationship with Him up till now.
Second, Jesus supernaturally opened their minds to understand the scriptures. Again, that is not the common practice today. The disciples in that day needed immediate understanding of the scriptures so they might understand how Jesus fulfilled what was written in them. Today we have a learning curve. But the power of God's word is still as potent to dispel doubts. Once we understand the scriptures, written before and after Jesus' life on earth, reveal God's plan of redemption through Jesus It builds our faith that God is in The scriptures reveal God's sovereignty over history and that His purposes will always be fulfilled. We can move past doubt to faith, even if what we are seeing doesn't line up with what we know to be true about God.
Third, Jesus promises the Holy Spirit to live in us. The disciples had to wait for that, we are given the Holy Spirit to dwell in us at the point of conversion. We literally have God living in us in the form of the Holy Spirit and Jesus interceding for us at the right hand of the Father. The Holy Spirit is our guide who leads us into all truth. Ask the Holy Spirit to strengthen your faith and overcome your doubts.