Eventually God’s presence moved into a permanent structure that King Solomon had built. After this new glorious temple was built, a worship service was held in which the ark of the covenant was brought into the new Holy of Holies. Songs were played by a giant band and sacrifices were made beyond number as the celebration continued. It was then that God’s presence invaded this new sacred space; for “the house of the Lord, was filled with a cloud, so that the priests could not stand to minister because of the cloud, for the glory of the Lord filled the house of God” (2 Chron 5:13-14).
But eventually this temple was destroyed and replaced by a second temple that Herod helped build closer to Jesus’ time. This will be the same temple that Jesus enters and flips tables in, though it’s a question as to how many people saw the outburst as the outer court of the temple was enormous—somewhere around 35 acres.
There were four major sections to this particular temple: The court of the Gentiles where people outside of the Jews were allowed to be; the court of women where Jewish women were permitted to go; the court of Israel where circumcised Jewish males were permitted to go; and the Holy of Holies which was still the most sacred space of the temple that only priests were allowed to enter.
This sacred space was guarded, with a sign hanging inside that had on it a warning in Greek, Latin and Aramaic: “No foreigner may enter within the railing and enclosure that surround the Temple. Anyone apprehended shall have himself to blame for his consequent death.” (Edwards, James R. The Gospel According to Mark. Mark 11:15–16.)
All of this being said, however, there’s no affirmation that God’s presence was ever truly believed to have been in the second temple. We do not have stories evidencing that His glory or presence were ever imparted to this structure.