Indwelling sin is compared to a person, a living person, called "the old man," with his faculties, and properties, his wisdom, craft, subtlety, strength; this, says the apostle, must be killed, put to death, mortified,— that is, have its power, life, vigour, and strength, to produce its effects, taken away by the Spirit. It is, indeed, meritoriously, and by way of example, utterly mortified and slain by the cross of Christ; and the “old man” is thence said to be “crucified with Christ,” Rom. vi. 6,and ourselves to be “dead” with him, verse 8, and really initially in regeneration, Rom. vi.3–5, when a principle contrary to it, and destructive of it, Gal. v. 17, is planted in our hearts; but the whole work is by degrees to be carried on towards perfection all our days. -Mortification of Sin I.4.3, emphasis mine
He tells us whence it is that we have this baptism into the death of Christ, verse 6; and this is from the death of Christ itself: "Our old man is crucified with him, that the body of sin might be destroyed;" συνεσταυρώθη, "is crucified with him," not in respect of time, but causality. We are crucified with him meritoriously, in that he procured the Spirit for us to mortify sin; efficiently, in that from his death virtue comes forth for our crucifying; in the way of a representation and exemplar we shall assuredly be crucified unto sin, as he was for our sin. This is that the apostle intends: Christ by his death destroying the works of the devil, procuring the Spirit for us, hath so killed sin, as to its reign in believers, that it shall not obtain its end and dominion. - XIV, emphasis mine
Notwithstanding the meritorious mortification, if I may so speak, of all and every sin in the cross of Christ; notwithstanding the real foundation of universal mortification laid in our first conversion, by conviction of sin, humiliation for sin, and the implantation of a new principle opposite to it and destructive of it; — yet sin doth so remain, so act and work in the best of believers, whilst they live in this world, that the constant daily mortification of it is all their days incumbent on them. - II.6, emphasis mineIf you say that "the old has passed away" (2 Cor 5:17) 100% without qualification in some sense, then John Owen disagrees with you. He says that the "old man" is crucified with Christ--"utterly" dead and gone--in these qualified senses:
- in example
But as far as being "really" dead and gone, it is only true "initially." Regeneration is not a complete change but "the implantation of a new principle." It is not a new structure altogether but only a new "foundation."
This should be encouraging for the newer believer who sees the same old sins creeping back when he thought they were totally gone. Don't worry that maybe you aren't saved. This is normal.