Through the Soul King who has a stronger Almighty.
Basically when they sealed him in that crystal at his choice, the Ancestors of the Noble Family basically put him in a state between life and death by basically removing his limbs and removing his organs including his brain(Which became Gremmy for the Brain, Gerard for the Heart, the Left Arm became Pernida and the Right Arm Mimihagi) and he can't do shit with the Almighty anymore despite us literally seeing he has The Almighty and a stronger version than Yhwach in the Manga(4 Pupils to Yhwach's 3) AND still being alive the entire time.
EDIT: This obviously happened to Yhwach afterwards as it was stated that an Almighty Users legit cannot die and will always come back(which is what happened to Yhwach when he fought Yamamoto all of those years ago) but you can do that to permanently take them down or make them worthless.