“I am the true vine, and my Father is the vinedresser. Every branch in me that does not bear fruit he takes away, and every branch that does bear fruit he prunes, that it may bear more fruit.
(John 15:1-2 ESV)

Pruning seems counter intuitive but it results in more fruit. The gardener knows how to prune. God prunes us through Jesus’ words as well as through circumstances, suffering etc. It seems wrong and even painful to us but God knows best how to make us more fruitful. Does something in God's word challenge you or disturb you? God is pruning you. Are you going through difficult circumstances? God's desire is that you would bear more fruit due to that process. We don't get the big picture, but we are just the plants. God is the gardener and he knows what he is doing.