The initial filling of the Holy Spirit and the baptism of the Holy Spirit are two distinct events, with different effects and purposes.
The initial filling happens the moment a person receives Jesus Christ as Lord and Savior, by faith. Before salvation, we were spiritually dead in sin, but once we are born again by the Spirit, we are made spiritually alive in Him. (Jn 3:6; Rom 10:9; Eph 2:1; Col 2:13.) At the moment of salvation, the Holy Spirit breathes the breath of His spiritual life into us, animating us with this life. This is the moment we come alive to a new life in Christ. We become a new creation. (2Cor 5:17; Eph 4:24; 1Pet 1:3; Col 3:10.)
We read this in John 20 where John explains the days following Jesus’ crucificion: Jesus’ disciples were hiding in a securely locked house. They were hiding from the Jewish leaders, fearing for their lives. John writes, the resurrected Lord Jesus appeared to them, alive and in power. He showed them His nail marked hands and the wound on His side saying, “Peace be with you. As the Father has sent Me, so I am sending you.” And with that He breathed on them and said, “Receive the Holy Spirit” (Jn 20:21-22).
This is the moment the disciples saw the risen Lord Jesus for the first time. (Other than Mary and the two disicples on the road to Emmaus, Mk 16:9-13; Lu 24:13-35.) This is the moment they were born again, born of the Spirit, and became a new creation. Previous to this, during the years they had followed Jesus as He ministered, they were not yet born again, they were not yet the new creation. Jesus had to first die and be raised from the dead to inaugurate the new covenant in His blood before they could be made into a new creation man.
Jesus breathing on His disciples reversed what Adam had lost. When God created Adam, He formed him from the dust and “breathed the breath of life” into him (Gen 2:7). But when Adam sinned, he spiritually died, and death came to all men after Adam through this first sin (Rom 5:12; 1Cor 15:21-22).
Jesus reversed this, FULLY!
In John 20, the resurrected Lord Jesus Christ, who is God, once more breathed life into men, re-animating us with His life.
He was able to do this because of His sacrifice which cannot be undone. This new life cannot be taken away from us like it was with Adam. We are marked with a seal of ownership over our hearts. We belong to Christ. Purchased with His blood. And we have received the Holy Spirit: “[We] also were included in Christ when [we] heard the message of truth, the gospel of [our] salvation. When [we] believed, [we] were marked in Him with a seal, the promised Holy Spirit, who is a deposit guaranteeing our inheritance…” (Eph 1:13-14). This is the initial filling of the Holy Spirit of every believer. With this seal we are now marked by God as His own, permanently. (See also 2 Cor 5:5; Eph 4:30; 1Pet 1:5; Rev 7:3-4, 9:4, 14:1, 22:4.)
This initial filling event occurs previous to the baptism of the Holy Spirit event. It did for Jesus’ disciples. They waited six weeks (Jn 20, Acts 1 and 2). Paul waited three days (Acts 9). For some, it may be months or even years because they have had no one tell them there is a powerful baptism waiting for them (Acts 19:1-5). Sometimes these two events occur simultaneously. First comes the born again experience, being made into the new creation, as we receive the breath of the Spirit of life into our hearts. Then the baptism comes upon the new creation man.
If you have not yet read Acts 2, please do. It is the testimony of the Holy Spirit coming powerfully to baptize the disciples, and the world has never been the same since.