PSALM 99 - Merciful Holiness

Summer Psalms 2025  •  Sermon  •  Submitted   •  Presented   •  39:21
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The fearsome holiness of God that causes us to tremble is mediated to us through the mercy of God found in the person of Christ

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Introduction

I don’t know about you, but I’m pretty burned out on politics these days. All of the hype and excitement over the results of the election—even with all the good things that have come out of it—is starting to wear a bit thin, as you watch campaign promises starting to get broken like always (“Epstein files?? WHAT Epstein files???”)
It’s another reminder that every administration (and every Congress and every judiciary) are all made up of fallible, unreliable, fallen men. What J. C. Ryle said about church leaders is just as true of the civil magistrate:
The best of men are only men at their very best. Patriarchs, prophets, and apostles, – martyrs, fathers, reformers, puritans, – all are sinners, who need a Savior: holy, useful, honorable in their place – but sinners after all. (Expository Thoughts on the Gospels, Matthew).
There is a similar lesson to be learned by reading through the accounts of the kings of Israel and Judah in the Old Testament—time after time we read of kings who carried out wonderful reforms and saw great revivals of faithfulness to YHWH, but then fell away into idolatry and wickedness. Think of King Joash, for instance, in 2 Chronicles 24, who oversaw a major rehabilitation of the Temple of Solomon and reformed covenant worship in Jerusalem. As soon as his mentor Jehoiada the priest died, though, Joash went right back to worshipping the false gods of the Canaanites (2 Chronicles 24:8-19). The entire record of human history right up to the present day shows us that there is no human ruler that will not eventually disappoint us in one way or another.
That is why the psalms we have been studying this summer—the so-called “enthronement psalms” that declare “YHWH reigns!” (v. 1, cp. Ps. 93:1; Ps. 96:10; Ps. 97:1) are assembled here in Book IV of the Psalms as part of the “Back to the Foundations” theme of this section of the Psalter. The exiles returning from Babylon to Jerusalem would sing these psalms to celebrate the restoration of the worship of YHWH on Mount Zion:
Psalm 99:2 LSB
Yahweh is great in Zion, And He is exalted above all the peoples.
Once again, the theme of this psalm is the holiness of YHWH—we see it repeated throughout these verses:
Psalm 99:3 LSB
Let them praise Your great and awesome name; Holy is He.
Psalm 99:5 LSB
Exalt Yahweh our God And worship at the footstool of His feet; Holy is He.
Psalm 99:9 LSB
Exalt Yahweh our God And worship at His holy mountain, For holy is Yahweh our God.
The exiles returning to Jerusalem from captivity were rejoicing in the holiness of YHWH. But as we saw a few weeks ago, the holiness of God—unchecked and unfiltered—will utterly unmake sinful creatures like us! Even here in the first verse of our text we see the effects of coming into the presence of YHWH’s holiness:
Psalm 99:1 LSB
Yahweh reigns, let the peoples tremble; He sits enthroned above the cherubim, let the earth quake!
We may groan under the fickle and morally shaky leaders of our present hour, but at least they are mortals like us! It is a hardship to bear the consequences of flawed and fallen politicians, but when we look to the perfect and utterly just and righteous King over all Creation, we find that His presence is even more unbearable to us!
What I aim to help you see here in this psalm today—what I want you to rejoice in and find your treasure in today—is that
Without the MERCY of God we cannot bear the HOLINESS of God
Now, commentators have different opinions on how this psalm can be divided up—some look at each repetition of “Holy is He” and suggest there are three divisions. But I think it’s a lot more straightforward than that—we see two verses in particular that echo each other. Verse 5:
Psalm 99:5 LSB
Exalt Yahweh our God And worship at the footstool of His feet; Holy is He.
And verse 9: Ps 99:9
Psalm 99:9 LSB
Exalt Yahweh our God And worship at His holy mountain, For holy is Yahweh our God.
So it seems as though the psalmist is setting this psalm into two sections, and when we look at the content of each section we see the way the main thrust of the psalm is developed. Verses 1-5 are a description of what sets God apart in His holiness, and verses 6-9 are how we are to respond to God’s holiness (and more specifically, how He responds to us!)
So let’s look at each half of the psalm in turn. First, we are called to

I. Exalt the holy MAJESTY of the King (Psalm 99:1-5)

Psalm 99:1–5 LSB
Yahweh reigns, let the peoples tremble; He sits enthroned above the cherubim, let the earth quake! Yahweh is great in Zion, And He is exalted above all the peoples. Let them praise Your great and awesome name; Holy is He. The strength of the King loves justice; You have established equity; You have done justice and righteousness in Jacob. Exalt Yahweh our God And worship at the footstool of His feet; Holy is He.
Consider first in these verses
The SOVEREIGN POWER of God’s reign (cp. Daniel 4:35)
The earth itself quakes under His holy reign—the natural world around us is guided and sustained moment by moment by His rule over it. The Sun rises each morning because He summons it; the tides rise and fall because He commands them; when a volcano erupts it is in response to His order; when the tsunami hurls itself against the shore, it has done so at His order.
As one preacher put it:
To see God in little things, to believe that there is as much the presence of God in a limb falling from the elm as in the avalanche which crushes a village; to believe that the guidance of every drop of spray, when the wave breaks on the rock, is as much under the hand of God as the steerage of the mightiest planet in its course… (Spurgeon, C. H. (1882). Farm Sermons (pp. 221–222). Passmore and Alabaster.)
There is nowhere to go to be out from under the power of God’s sovereign hand—from tectonic plates to tumors, from pandemics to paper-cuts, all of it is in His hand, and there is no one who can thwart Him:
Daniel 4:35 LSB
“And all the inhabitants of the earth are accounted as nothing, But He does according to His will in the host of heaven And among the inhabitants of earth; And no one can strike against His hand Or say to Him, ‘What have You done?’
The sovereign power of God’s reign is seen in the natural world around us, and the psalmist says that power brings forth
The TREMBLING PRAISE of God’s subjects (cp. 2 Chron. 36:14-16)
Psalm 99:1 LSB
Yahweh reigns, let the peoples tremble; He sits enthroned above the cherubim, let the earth quake!
They tremble not just because of the immense and unstoppable power of God in Creation, but they tremble because they understand that He is a just God:
Psalm 99:4 LSB
The strength of the King loves justice; You have established equity; You have done justice and righteousness in Jacob.
The psalmist praises YHWH for the way He has “done justice and righteousness in Jacob (Israel).” But consider for a moment what that justice entailed. At the end of 2 Chronicles, the final fall of Jerusalem and the Kingdom of Judah—the last remnants of the covenant people of YHWH—is described this way:
2 Chronicles 36:14–16 LSB
Furthermore, all the leaders of the priests and the people were very unfaithful following all the abominations of the nations; and they defiled the house of Yahweh which He had set apart as holy in Jerusalem. And Yahweh, the God of their fathers, sent word to them again and again by the hand of His messengers, because He had compassion on His people and on His habitation; but they continually mocked the messengers of God, despised His words and scoffed at His prophets, until the wrath of Yahweh arose against His people, until there was no remedy.
YHWH warned Jacob over and over again about the consequences for rebelling against Him; that His holiness demanded punishment for their sin. But they did not listen—they mocked, despised and scoffed until His holy wrath was aroused and He brought them to justice.
In his 1785 pamphlet Notes on Virginia, Thomas Jefferson wrote, “Indeed I tremble for my country when reflect that God is just: that his justice cannot sleep for ever...” Here in Psalm 99 we see the terrible example of Israel, when the holy justice and righteousness of YHWH was aroused toward His people.
There is no way for us to bear the holiness of God unless it is tempered by the mercy of God. The psalmist calls us to exalt the holy majesty of our King in verses 1-5. And then starting in Verse 6 we are called to

II. Exult in the holy MERCY of the King (Psalm 99:6-9)

Psalm 99:6–9 LSB
Moses and Aaron were among His priests, And Samuel was among those who called on His name; They would call upon Yahweh and He would answer them. He would speak to them in the pillar of cloud; They kept His testimonies And the statute that He gave them. O Yahweh our God, You answered them; You were a forgiving God to them, And yet an avenger of their evil deeds. Exalt Yahweh our God And worship at His holy mountain, For holy is Yahweh our God.
There is such a shift in tone between verses 1-5 and the rest of the psalm, some textual critics claim that Psalm 99 was actually two different psalms that were somehow “mistakenly” spliced together as one. To be fair, there really is a dramatic change—the first five verses describe YHWH in His exalted position “far above all the peoples”, with Mount Zion and the Temple being described as “the footstool of His feet”. He is lofty, far removed from the sin and wickedness of this world, His justice and righteousness going before Him and wiping out all rebellion and faithlessness.
But then we read about Moses and Aaron and Samuel—
Psalm 99:6–7 LSB
...They would call upon Yahweh and He would answer them. He would speak to them in the pillar of cloud...
He is the transcendent God Who dwells far above all of the peoples, and yet He was present to hear the prayers of His people! See here that the only way we can bear the holiness of our King is because His holiness comes to us through His mercy toward us! He is the God Whose justice and righteousness goes before Him in terrible splendor, but at the same time
He ANSWERS the ADVOCATE’S prayer (vv. 6-7)
Whenever a psalm specifically names individuals in the Bible it is worth tracking down how they fit in the theme of the psalm. The theme of Psalm 99 is the mercy that a holy God shows His people. And when we look at the accounts of each of these men, we see that each one of them “stood in the gap when the wrath of God broke forth” (Spurgeon).
In Exodus 32:30-34, after the people had committed idolatry by worshipping the golden calf, Moses prayed for God to spare them:
Exodus 32:31–32 LSB
Then Moses returned to Yahweh and said, “Alas, this people has committed a great sin, and they have made gods of gold for themselves. “But now, if You will forgive their sin—but if not, please blot me out from Your book which You have written!”
And YHWH heard Moses’ prayer and spared the people.
In the same way, Aaron offered the blood of the sacrifice each year on the Day of Atonement
Leviticus 16:3 LSB
“Aaron shall enter the holy place with this: with a bull from the herd for a sin offering and a ram for a burnt offering.
Aaron stood between the people and the holiness of YHWH with the blood of the sacrifice—
Leviticus 16:16 LSB
“So he shall make atonement for the holy place because of the uncleanness of the sons of Israel and because of their transgressions in regard to all their sins; and thus he shall do for the tent of meeting which abides with them in the midst of their uncleanness.
Leviticus 16:30 LSB
for it is on this day that atonement shall be made for you to cleanse you; you will be clean from all your sins before Yahweh.
And decades later, the prophet Samuel also stood between the holiness of YHWH and His sinful people after they had strayed from YHWH and worshipped the false gods of the Canaanites:
1 Samuel 7:3 LSB
Then Samuel spoke to all the house of Israel, saying, “If you are to return to Yahweh with all your heart, then remove the foreign gods and the Ashtaroth from among you and set your hearts toward Yahweh and serve Him alone; and He will deliver you from the hand of the Philistines.”
1 Samuel 7:9 LSB
And Samuel took a suckling lamb and offered it for a whole burnt offering to Yahweh; and Samuel cried out to Yahweh for Israel, and Yahweh answered him.
In each case, the holiness of YHWH would have broken out against the sins of the people and utterly wiped them out—and He would have been utterly just and righteous to do so. But the holiness of YHWH toward His people is always tempered by His mercy to His people—He appears in the cloudy pillar so that He can draw near to His people to hear and answer them!
Psalm 99:8 LSB
O Yahweh our God, You answered them; You were a forgiving God to them...
Exult in the mercy of your holy King, Christian—He answers the advocate’s prayer, and
He FORGIVES the HOPELESS sinner (vv. 8-9)
Psalm 99:8–9 LSB
O Yahweh our God, You answered them; You were a forgiving God to them, And yet an avenger of their evil deeds. Exalt Yahweh our God And worship at His holy mountain, For holy is Yahweh our God.
And here is where the unstoppable holiness of YHWH and the bottomless mercy of YHWH meet—YHWH is a forgiving God to them, and yet He avenges their evil deeds. He is utterly holy and righteous and just—He will not bear to look upon evil. The holiness of God will (and must) utterly destroy sin and ever sinner that has sinned against Him.
And yet YHWH is said here to be a forgiving God—He takes away their guilt and sin and accepts their cry for repentance. Their sin and their wickedness and rebellion against Him is simply taken away. It is easy to understand how God can be either holy or forgiving; but how can God say “The soul that sins, it shall surely die” and “I am compassionate and gracious, slow to anger, and abounding in lovingkindness and truth”? (Ex 34:6)
The answer to this tension can be found woven throughout Psalm 99. It begins with the first verse:
Psalm 99:1 LSB
Yahweh reigns, let the peoples tremble; He sits enthroned above the cherubim, let the earth quake!
That YHWH is enthroned “above the cherubim” doesn’t just mean that He is above all angelic beings—this is a reference to the throne of YHWH that sat atop the Ark of the Covenant, where the wings of the cherubim covered the mercy seat. The holiness of YHWH is a merciful holiness toward His people.
This entire psalm is filled with images of the Temple in Jerusalem—King David called the Temple “the footstool of YHWH’s feet” in 1 Chronicles 28:2
1 Chronicles 28:2 LSB
Then King David rose to his feet and said, “Listen to me, my brothers and my people; I had it within my heart to build a house of rest for the ark of the covenant of Yahweh and for the footstool of the feet of our God....
And what does it mean to “worship at His holy mountain” in verse 9 but that His people are called to worship at the Temple that was built there? And when Aaron offered the blood of the sacrifice to turn aside the wrath of God against the people’s sin on the Day of Atonement, where did he splash that blood? On the mercy seat of the Ark! We cannot read Psalm 99 without being reminded of what was done on that mountain we are called to worship at—the blood of sacrifices flowed so freely out of that Temple that the brook flowing past in the valley below was named the Kidron Brook— kidron in Hebrew means dark or black—it was the “Black Brook” because of all of the blood that flowed into it from the Temple mount above!
The unflinching holiness of your King, Christian, means that He cannot look the other way; He is the avenger of evil deeds. And yet He is the God that is seated on the mercy seat, covered by the blood of the sin sacrifice. What this psalm foreshadows, what the Temple on Mount Zion pointed to, was the coming of the One Who would bear the fulness of YHWH’s holy wrath against sin, the One that would suffer the complete and total vengeance of YHWH against evil.
Jesus Christ is the Final Sacrifice—His death meant that God’s wrath against your sin was completely satisfied. And in His resurrection from the dead three days later, He rose to the right hand of the Father in order to be your advocate:
1 John 2:1–2 LSB
... if anyone sins, we have an Advocate with the Father, Jesus Christ the righteous; and He Himself is the propitiation for our sins, and not for ours only, but also for those of the whole world.
He is the advocate that stands between you and the wrath of God that you deserve. He is your refuge from the unflinching holiness of YHWH; in Jesus Christ, you have received the holiness of YHWH Himself!
1 Peter 1:16 LSB
because it is written, “You shall be holy, for I am holy.”
Christian, one of the most crucial truths that you can discipline your mind and heart to embrace is that in Jesus Christ you have been given the holiness of God:
Ephesians 1:4 LSB
just as He chose us in Him before the foundation of the world, that we would be holy and blameless before Him in love,
The mercy of God toward you in Christ means that you are holy. And what that means is that you are now defined by that holiness. You are now defined by what Christ has done for you. And this means that you are not defined by your pain. You are not defined by your trauma. You are not defined by your failures. You are not defined by your past. You are not defined by your fears. You are not defined by your lusts. You are not defined by any of it. Christian—you are what God says you are. And He says that you have been given His holiness. The very holiness of God that causes the peoples to tremble and the earth to quake and the heavens to rejoice and the mountains to clap their hands and the seas to roar—you are holy in His sight.
The mercy of God toward you in Christ means that you have an Advocate in Him. He has placed Himself between you and the unflinching holiness of YHWH in order to plead for you. He sees your struggles with sin, He sees your failures, He sees your weaknesses and your stumbles, and He brings His prayers for you to Your Father in Heaven. So do not grow weary in your battles with sin. Do not give up striving for the holiness that He has promised you. Do not be discouraged at how little progress you see in your striving. Do not grow weary in well-doing, keep resting on His work, keep clinging to the blood that was shed to wash away your past. Be of good cheer in your fight, Christian, for “...He who began a good work in you will perfect it until the day of Christ Jesus.” (Phil. 1:6).
And friend if you are here apart from Christ this morning, can’t you see the amazing treasure that you are being offered here this morning? That the holiness of God—so powerful and so unstoppable that your sinful soul would vanish before Him like a snowflake in a furnace—that holiness of God is being offered to you right now by the mercy of Jesus Christ! When you call upon Him in repentance—just as Moses and Aaron and Samuel did—then He has promised to hear you! He will answer you, He will be a forgiving God to you—He has avenged all your evil deeds on the head of Christ on the Cross, and when you call out to Him for forgiveness, He will hear you! He has taken His stand between your sin and the wrath of God, and He will cleanse you from all of your guilt and shame and regret and trauma and pain and hopelessness and give you His holiness instead!
Jesus promises you this morning in John 6:37 “All that the Father gives Me will come to Me, and the one who comes to Me I will never cast out.” Do not leave here today without knowing that the holiness of God will be toward you a merciful holiness, given to you freely by your merciful Savior, Jesus Christ!
BENEDICTION:
Hebrews 13:20–21 LSB
Now the God of peace, who brought up from the dead the great Shepherd of the sheep through the blood of the eternal covenant, our Lord Jesus, equip you in every good thing to do His will, by doing in us what is pleasing in His sight, through Jesus Christ, to whom be the glory forever and ever. Amen.

QUESTIONS FOR REFLECTION AND DISCUSSION

How does God’s sovereign holiness as our King give you reassurance in light of the fallenness of our political leaders and current events?
How does your understanding of God’s holiness affect the way you relate to Him? How should the holiness of God shape the way we approach Him in worship?
What is the significance of YHWH’s enthronement “above the cherubim”? How does this image help us connect God’s holiness with His mercy?
How can God be a “forgiving God” while at the same time “avenge our evil deeds”?
In what ways do Moses, Aaron and Samuel point ahead to the ministry of Christ? How does Christ’s priestly work as an Advocate for you strengthen your daily resolve to fight sin and strive for the holiness He has promised?
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