Sounds mystical, intangible, and mysterious, doesn’t it? But it doesn’t have to!
The idea of praying in the Spirit is certainly found in Scripture, in places like Ephesians 6:18, where Paul writes about:
praying at all times in the Spirit, with all prayer and supplication.
or Jude 20, which reads:
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.
But what does it mean? In an effort to provide an answer, let’s ask the opposite question: what would it mean to not pray in the Spirit? What would that look like?
Praying without being filled by the Spirit and with the help of the Spirit would mean our prayers wouldn’t be informed by spiritual insight from the Word of God. If we didn’t pray in the Spirit, we wouldn’t know what to pray for. If we weren’t praying in the Spirit, our prayers wouldn’t be controlled by the Spirit, meaning we wouldn’t be submissive to God’s will, such that, our praying would sound more like telling God what we think He should do rather than surrendering ourselves to His purposes. Praying apart from the Spirit would mean that we’re overlooking our sinfulness and weakness, rather than depending on the Spirit to “help us in our weakness. For we do not know what to pray for as we ought, but the Spirit himself intercedes for us with groanings too deep for words (Romans 8:28).” Praying apart from the Spirit is to pray, in effect, without access to the Father (see Ephesians 2:18). And we could continue in this vein for quite some time, which changes the question to “How could we ever not pray in the Spirit?”
Praying in the Spirit then is an expression of our utter dependance on Him as we ask Him to fill us, invite Him to change us, even as we pray, because we are in need of supernatural transformation. Bryan Chapell writes in his commentary on Ephesians,
We should understand that there is many a cold heart ritualistically praying and reading Scripture in the vain expectation that the labor itself will produce godly love and spiritual power. We pray in the Spirit because we believe that the Spirit alone can so radically change the heart as to make it truly desire the things of God.
And as he points out, this is exactly work of the Spirit Paul prays for in the lives of the Ephesians in 3:14-21:
For this reason I bow my knees before the Father, from whom every family in heaven and on earth is named, that according to the riches of his glory he may grant you to be strengthened with power through his Spirit in your inner being, so that Christ may dwell in your hearts through faith – that you, being rooted and grounded in love, may have strength to comprehend with all the saints what is the breadth and length and height and depth, and to know the love of Christ that surpasses knowledge, that you may be filled with all the fullness of God.
Is there any other hope for faithful, meaningful, God-honouring prayer than prayer in the Spirit? Certainly not!