The LORD’s holy enthronement strikes fear in the nations (Ps. 99:1-3)
These opening lines are a proclamation of the Lord’s kingly reign which sparks fear (“trembling”) in the nations. The fear of the nations may have to do with the establishment of justice among Jacob (v. 4). If the Lord will judge his people for their injustice, what will he do to the nations that do not fear him? The coming of the Lord is an occasion of joy for his people because he will vindicate his people (v. 4) but it is an occasion for trembling among the nations for the same reason.
The Lord’s reign is related to his holy presence in the midst of his people. His dwelling between the cherubim (v. 1) is a reference to the “atonement cover” of the ark of the covenant (Lev. 16:13). This way of referring to the Lord in the context of his reign is not uncommon (1 Sam. 4:4; 2 Sam. 6:2; 2 Kings 19:15; 1 Chron. 13:6; Ps. 80:1; Isa. 37:16) since the ark was the sign of the Lord’s presence and served as his throne (v. 5, cf. Ps. 132:7-8; 1 Chron. 28:2).
The opening stanza contains a paradox: The Lord dwells between the cherubim (v. 1) yet is high above all nations (v. 2). The might of the Lord God of Israel will be revealed in his justice; he is high above the nations because he holds them to account. The mercy and covenant faithfulness of the Lord God of Israel is revealed in his continuing presence in the midst of his people despite their sin.
The holiness of the Lord is the attribute praised above all others in this psalm. That the Lord is holy emphasizes the distinct qualitative difference between God and man. This means that one’s relationship with the Lord is not to be taken casually. The nations must not take the Lord lightly because his holiness requires him to judge their wickedness and the oppression of his people. His own people, however, are not exempt because the Lord will judge their deeds, as well (v. 8).
The LORD’s holy might brings justice to Israel (Ps. 99:4-5)
The Lord’s holiness is what will bring justice to his people. His holiness is what drives his justice and strength and this characteristic will result in justice for his people.
The Lord’s holiness is what has established his law (since the law is an extension of his holy character). That the Lord in his strength “loves justice” (v. 4) shows that his might is devoted to doing what is right and maintaining right among his people and, by extension, his realm which is ultimately the entire world.
The Lord’s people are called to worship him because he is holy. The first portion of this psalm contains this refrain twice (vv. 3, 5). The reason stated for this praise, worship, and exaltation is the holiness of the Lord. Because the Lord is holy, his people should remember how great and fearsome is his name, they should praise and exalt him and worship him in the place he has prescribed: his holy footstool (another reference to the ark of the covenant; cf. Psa. 132:7).