The concept of praying in the Spirit is mentioned three times in the New Testament. The first occurrence is found in 1 Corinthians 14:15: "What am I to do? I will pray with my spirit, but I will pray with my mind also; I will sing praise with my spirit, but I will sing with my mind also." In this context, Paul is saying that praying in the Spirit is good, but something nobody understands is not much use to anyone (1 Corinthians 14:17). Paul's desire was to love the Lord with all his soul, mind, and strength (Mark 12:29–31; Matthew 22:37–40). In order to do this, both his prayers and his speech needed to be meaningful to both the heart and the mind. Paul's reference to "praying in the spirit" here cannot be taken to mean something which the praying person themselves does not understand.
The second time praying in the Spirit is mentioned is found in Ephesians 6:18. Here, Paul shares, "And pray in the Spirit on all occasions with all kinds of prayers and requests" (NIV). In this context, Paul instructed how to pray for him during his missionary efforts "for which [he was] an ambassador in chains" (Ephesians 6:20). He wanted believers to pray in the Spirit that God would allow him to speak the gospel boldly during his time in Rome.
The third time praying in the Spirit is mentioned is in Jude 1:20–21. Jude shares, "But you, beloved, building yourselves up in your most holy faith and praying in the Holy Spirit, keep yourselves in the love of God, waiting for the mercy of our Lord Jesus Christ that leads to eternal life." Here, Jude includes all three Persons of the Triune God—God the Father, God the Son, and God the Spirit—to emphasize the important role each has in our lives. Through growth and prayer, believers were to increase in love for God as they prepared for eternity with the Lord.
Some interpret "praying in the Spirit" as a reference to praying in tongues or other languages that is mentioned in 1 Corinthians 14. However, the context of that chapter actually seems to be contrasting "praying in the Spirit" with speaking in tongues. In particular, Paul makes the point—of both—that there must be a message understood in order for there to be any meaning. Those who prayed in another tongue or language did so for the benefit of unbelievers (1 Corinthians 14:22). Praying, or speaking, in words nobody understands is useless, and not commended anywhere in the Bible.
In addition, speaking in a tongue or language was mentioned as a gift available only to some in the church (1 Corinthians 12:7–11). In contrast, praying in the Spirit was a command given to all believers. Therefore, praying in the Spirit must be a different activity as all Christians were taught and expected to do so.
Praying in the Spirit is the biblical teaching of prayer with both emotion and intellect with complete dependence upon the Spirit of God to help pray appropriately to God the Father through Jesus the Son of God. When we pray in accordance with God's Spirit we can pray according to God's will and be confident of His perfect answer to our requests.
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