God’s omnipresence means He is everywhere at all times, whether we perceive Him or not, while His manifest presence is when He makes His nearness clear and undeniable. The Holy Spirit reveals God’s manifest presence through comfort, answered prayer, and transformed lives.
The word "manifest" is defined as "clear or obvious to the eye or mind." God's manifest presence is what believers see and know of Him. This is different from God's omnipresence. The meaning of the word omnipresence is "everywhere present." The Bible teaches that this is a key attribute of God (Psalm 139:7-10). God is in all places simultaneously. God's omnipresence is not altered by the observer. At times, though, Scripture records God’s manifest presence, i.e., special circumstances during which He made Himself known to someone through the senses. Examples include God making Himself known to Moses in the burning bush (Exodus 3), when Jesus took on human form (John 1:14), and the indwelling presence of the Holy Spirit in believers’ lives (1 Corinthians 6:19). Unbelievers may deny God’s existence, but that does not change His omnipresence. God's manifest presence, on the other hand, is sometimes experienced and other times not.
The manifest presence of God is not necessarily, or even usually, something experienced empirically. That is, it cannot be felt by the senses or recorded by some physical means. But nonetheless, it is experienced. It is felt in the inexplicable comfort God gives in the midst of tragedy. It is experienced in answered prayer. It is experienced in changed lives.
God’s presence never leaves a believer nor changes; however, our awareness of His activity in our lives might. Seasons of trial or distraction can dull our sensitivity, while times of prayer, worship, and obedience often sharpen it. The Holy Spirit draws near to remind us of God’s promises and to refocus us on His truth. The manifest presence of God is less about a feeling and more about the deep assurance that He is with us, working in ways unseen yet undeniably real. Ultimately, His presence is a gift that sustains, strengthens, and anchors us, regardless of what we see or feel.
The difference between the manifest presence of the Holy Spirit and God's omnipresence is that God's omnipresence is always there, despite the fact that we cannot always feel it. In other words, God's presence is everywhere, at all times, and with all of us, believer and unbeliever alike. Likewise, His Holy Spirit indwells believers at all times. But His manifest presence occurs in our lives as He chooses to reveal Himself. It is the appearance to the human mind or eye of the reality of His omnipresence and continual care: "...for he has said, 'I will never leave you nor forsake you'" (Hebrews 13:5).