I yow assoile [absolve], by myn heigh power -Yow that wol offre - as clene and eek as cleerAs ye were born.
What the Pardoner is describing is not actually a sufficient absolution. Because of original sin, everyone has an inherited guilt even when he's born. (Psalm 51:5: "Behold, I was brought forth in iniquity, and in sin did my mother conceive me.") No one is born "clene and... cleer."
Earlier in the tale, the Pardoner explains that his main motivation is money: "For myn entente is nat but for to winne, / And nothing for correccioun of sinne." He's not genuine in his position, and therefore it seems doubtful that his absolutions would carry any benefit, so he may mean exactly what he says: he will "absolve" you, but you will still be as filthy and sin-stained as before. He uses "clene and... cleer" ironically.
There's also the simple possibility that he doesn't understand these religious matters properly and he fully believes both that his all-consuming avarice can sit well alongside his occupation and that the absolution he offers will indeed cleanse the penitent.
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In his prologue, the Pardoner says that his theme is "Radix malorum est Cupiditas." In The Norton Critical Edition, there's a footnote for this that reads, "Avarice (the love of money) is the root of all evil (1 Timothy 6:10)." This is not entirely accurate.
The Pardoner's Tale and 1 Timothy 6:10 both have genitive plurals ("malorum"); it's "of evils." The Norton also pulls in "all" from 1 Timothy 6:10 ("radix enim omnium malorum est cupiditas" in the Vulgate, ῥίζα γὰρ πάντων τῶν κακῶν ἐστιν ἡ φιλαργυρία in the Greek) without making it clear that this is not present in what the Pardoner says. "Radix malorum est Cupiditas" is simply "Avarice is a root of evils," not "Avarice is a root of all evils."