The beginning of the verse is in various ways explained. Some make a stop after cleanse thus, "I will cleanse, yet their blood I will not cleanse;" as though God had said, that he would forgive heathen nations all their other wrongs, but could not forgive them the great cruelty they had exercised against his elect. So the sense would be, "Avarice may be borne, I could pass by robberies; but, since they slew my people, I am in this case wholly unforgiving." Hence, according to this view, God shows how precious to him is the life of his saints, inasmuch as he says, that he will not be pacified towards those ungodly men who have shed innocent blood. But this sense seems rather too forced. Others render thus, "Their blood will I cleanse, and will not cleanse," that is, "I will cleanse the Jews from their defilements, but I will not use extreme severity;" as he says also in Isaiah 48, I will not refine thee as gold or silver, for thou wouldest turn all into dross.' They hence think that God promises here such a cleansing of the Church, as that he would not use extreme rigor, but moderate his cleansing, as it is needful with regard to our defilements, of which we are all so full. But this sense seems to me more simple, -- that God would cleanse the blood which he had not cleansed; as though he said, "I have not hitherto cleansed the pollutions of my people; they are then become, as it were, putrid in their sins; but now I will begin to purify all their wickedness, that they may shine pure before me." There is a relative understood as is often the case in Hebrew. But nqh neke is taken in Jeremiah 30:11, in another sense, that God will exterminate his Church: but we cannot in this place elicit any other meaning than that God will cleanse his Church from pollutions; for the Prophet, no doubt, means the defilements of which the people were full. They will not, then, be able to enjoy the favor of God while lying in their filth. Now God, in promising to be a Redeemer, comes to the very fountain and the first thing, -- that he will wash away their filth; for how could God be the Redeemer of the people, except he blotted out their sins? For as long as he imputes sins to us, he must necessarily be angry with us, we must be necessarily altogether alienated from him and deprived of his blessing. He then does not say in vain that he will be a purifier; for when pollutions are cleansed, there follows another thing, which we have already noticed as to this, future redemption, and with this -- He at last concludes and says And Jehovah shall dwell in Zion. The Prophet recalls again the attention of the people to the covenant; as though he said, "God has willingly and bountifully promised all that has been mentioned, not because the people have deserved this, but because God has deigned long ago to adopt the children of Abraham, and has chosen mount Zion as his habitation." He shows then this to be the reason why God was now inclined to mercy, and would save a people, who had a hundred times destroyed themselves by their sins.

For I will cleanse her blood that I have not cleansed - The word rendered "cleansed" is not used of natural cleansing, nor is the image taken from the cleansing of the body. The word signifies only to pronounce innocent, or to free from guilt. Nor is "blood" used of sinfulness generally, but only of the actual guilt of shedding blood. The whole then cannot be an image taken from the cleansing of physical defilement, like the words in the prophet Ezekiel, "then washed I thee with water; yea, I thoroughly washed away thy blood from thee" Ezekiel 16:9. Nor again can it mean the forgiveness of sins generally, but only the pronouncing innocent the blood which had been shed. This, the only meaning of the words, fall in with the mention of the "innocent blood," for shedding which, Egypt and Edom had been condemned. The words are the same. There it was said, "because they have shed innocent blood; dam naki;" here, "I will pronounce innocent their blood, nikkethi damam." "How," it is not said. But the sentence on Egypt and Edom explains how God would do it, by punishing those who shed it. For in that He punishes the shedding of it, He declared the "blood" innocent, whose shedding He punished. So in the Revelation it is said, "I saw under the altar the souls of them that were slain for the word of God, and for the testimony which they held, and they cried with a loud voice, saying, How long, O Lord, holy and true, dost Thou not judge and avenge our blood on them that dwell on the earth?" Revelation 6:10-11. : "Then, at the last judgment, when the truth in all things shall be made manifest, He shall "declare the blood" of His people, who clave to Him and His truth, which blood their enemies thought they had shed justly and deservedly as the blood of guilty persons, to have indeed been innocent, by absorbing them from eternal destruction to which He shall then adjudge their enemies for shedding of it."
For - (literally and) the Lord dwelleth in Zion He closes with the promise of God's abiding dwelling. He speaks, not simply of a future, but of an ever-abiding present. He who is, the unchangeable God , "the Lord, infinite in power and of eternal Being, who gives necessary being to all His purposes and promises," dwelleth now in "Mount Zion, the city of the living God, the heavenly Jerusalem" (Hebrews 12:22; add Galatians 4:26; Revelation 3:12; Revelation 14:1; Revelation 21:2, Revelation 21:10), now by grace and the presence of His Holy Spirit, hereafter in glory. Both of the Church militant on earth and that triumphant in heaven, it is truly to be said, that the Lord dwelleth in them, and that, perpetually. Of the Church on earth will be verified what our Saviour Christ saith, "lo I am with you always, even unto the end of the world" Matthew 28:20; and of its members Paul saith, that "they" are "of the household of God, an holy temple in the Lord, in whom they are builded together for an habitation of God through the Spirit" Ephesians 2:19, Ephesians 2:21-22. Of the Church triumphant, there is no doubt, that "He" doth and will there dwell, and manifest His glorious presence forever, "in" whose "presence is the fullness of joy, and at His Right Hand" there are "pleasures for evermore" Psalm 16:1-11 :12. It is an eternal dwelling of the Eternal, varied as to the way and degree of His presence by our condition, now imperfect, there perfected in Him; but He Himself dwelleth on for ever. He, the Unchangeable, dwelleth unchangeably; the Eternal, eternally.
: "Glorious things are spoken of thee, thou city of God" Psalm 87:3 Jerusalem, our mother, we thy children now groan and weep in this valley of tears, hanging between hope and fear, and, amid toil and conflicts, "lifting up our eyes" to thee and greeting thee from far. Truly "glorious things are spoken of thee." But whatever can be said, since it is said to people and in the words of people, is too little for the "good things" in thee, which "neither eye hath seen, nor ear heard, nor hath entered into the heart of man" 1-Corinthians 2:9. Great to us seem the things which we suffer; but one of thy most illustrious citizens, placed amid those sufferings, who knew something of thee, hesitated not to say, "Our light affliction, which is but for a moment, worketh out for us a far more exceeding and eternal weight of glory" 2-Corinthians 4:17. We will then "rejoice in hope," and "by the waters of Babylon," even while "we sit and weep," we will "remember thee, O Zion. If I forget thee, O Jerusalem, may my right hand forget" her cunning. "Let my tongue cleave to the roof of my mouth, I do not remember thee, if I prefer not Jerusalem above my chief joy" Psalm 137:1-9.
O blessed longed-for day, when we shall enter into the city of the saints, 'whose light is the Lamb,' where 'the King is seen in His beauty,' where 'all tears are wiped off from the eyes' of the saints, 'and there shall be no more death neither sorrow nor pain, for the former things have passed away Revelation 21:23; Isaiah 33:17; Revelation 21:4. "How amiable are Thy tabernacle, O Lord of Hosts! My soul longeth, yea fainteth for the courts of the Lord; my heart and my flesh crieth out for the living God" Psalm 84:1-2. "When shall I come and appear before God?" Psalm 42:2, when shall I see that Father, whom I ever long for and never see, to whom out of this exile, I cry out, "Our Father, which art in heaven?" O true Father, "Father of our Lord Jesus Christ" (Romans 15:6,), "Father of mercies and God of all comfort!" 2-Corinthians 1:3. When shall 'I see the Word, who was in the beginning with God,' and who 'is God?' John 1:1. When may I kiss His sacred Feet, pierced for me, put my mouth to His sacred Side, sit at His Feet, never to depart from them? O Face, more Glorious than the sun! Blessed is he, who beholdeth Thee, who hath never ceased to say, 'I shall see Him, but not now; I shall behold Him, but not nigh' Numbers 24:17. When will the day come, when, cleansed from the defilement of my sins, I shall, 'with unveiled face, behold the glory of the Lord' 2-Corinthians 3:18, and see the sanctifying Spirit, the Author of all good, through whose sanctifying we are cleansed, that 'we may be like Him, and see Him as He is?' 1-John 3:2. 'Blessed are all they that dwell in Thy house,' O Lord, 'they shall ever praise Thee' Psalm 84:4; forever shall they behold Thee and love Thee."

For I will cleanse their blood - נקיתי nikkeythi, I will avenge the slaughter and martyrdom of my people, which I have not yet avenged.
Persecuting nations and persecuting Churches shall all come, sooner or later, under the stroke of vindictive justice.
For the Lord dwelleth in Zion - He shall be the life, soul, spirit, and defense of his Church for ever. This prophet, who has many things similar to Ezekiel, ends his prophecy nearly in the same way:
Ezekiel says of the glory of the Church, יהוה שמה Yehovah shammah, The Lord Is There.
Joel says, יהוה שכן בציון Yehovah shochen betsiyon, The Lord Dwelleth in Zion.
Both point out the continued indwelling of Christ among his people.

For I will (n) cleanse their blood [that] I have not cleansed: for the LORD dwelleth in Zion.
(n) He had allowed his Church before this to lie in their filthiness, but now he promises to cleanse them and to make them pure unto himself.

For I will cleanse their blood which I have not cleansed,.... Which some understand, as the Targum, of the Lord's, inflicting further punishments on the, enemies of his people, for shedding their innocent blood; and that he will not expiate their sins, nor hold them guiltless, or suffer them to go unpunished; but rather this is to be interpreted in a way of grace and mercy, as a benefit bestowed on Judah and Jerusalem, who are the immediate antecedents to the relative here; and in the words a reason is given why they should dwell safely and peaceably for ever, because the Lord will justify them from their sins; forgive their iniquities; cleanse them from all their pollution, signified by blood; of which grace they will have had no application made to them till this time; but now all their guilt and faith will be removed; and particularly God will forgive, and declare to be forgiven their sin of crucifying Christ; whose blood they had imprecated upon themselves and their children, and which has remained on them; but now will be removed, with all the sad effects of it. Though this may also refer to the conversion of the Gentiles, and the pardon of their sins, and the sanctification of their persons, in such places and parts of the world, where such blessings of grace have not been bestowed in times past for many ages, if ever;
for the Lord dwelleth in Zion; and therefore will diffuse his grace, and spread the blessings of it all around: or "even the Lord that dwelleth in Zion" (d); he will do what is before promised; being the Lord, he can do it; and dwelling in Zion his church, it may be believed he will do it; and this will be for ever, when his Shechinah shall return thither in the days of the Messiah, as Kimchi observes.
(d) "even I the Lord", margin of our Bibles.

cleanse . . . blood . . . not cleansed--I will purge away from Judah the extreme guilt (represented by "blood," the shedding of which was the climax of her sin, Isaiah 1:15) which was for long not purged away, but visited with judgments (Isaiah 4:4). Messiah saves from guilt, in order to save from punishment (Matthew 1:21).

Joel 3:21 does not contain the announcement of a still further punishment upon Egypt and Edom, but simply the thought with which the proclamation of the judgment closes - namely, that the eternal desolation of the world-kingdoms mentioned here will wipe out all the wrong which they have done to the people of God, and which has hitherto remained unpunished. But Zion will rejoice in the eternal reign of its God. Jehovah dwells upon Zion, when He manifests Himself to all the world as the King of His people, on the one hand by the annihilation of His foes, and on the other hand by the perfecting of His kingdom in glory.

And I will cleanse - Purge away both by the spirit of sanctification and by free pardon in the blood of the redeemer. Their blood - Their sinfulness, which before I had not taken away.