“having the golden altar of incense and the ark of the covenant covered on all sides with gold, in which was a golden urn holding the manna, and Aaron’s staff that budded, and the tablets of the covenant” (Hebrews 9:4 ESV).
At the heart of the Holy of Holies stood the ark of the covenant. The ark was a chest that was constructed of acacia wood and overlaid with gold according to Exodus 25:10-22. The top (or lid) of the ark was known as the mercy seat (Exodus 25:17), a term that communicated the image of a sovereign authority who pardoned the sins of His people under the Old Covenant.
Two angelic beings known as cherubim were positioned above the ark at either end. Humanity first encountered these angelic cherubim when God stationed them “…east of the Garden of Eden, with a flaming sword to guard the entrance to the Tree of Life” (Genesis 3:24 TLB). The prophet Ezekiel also interacted with cherubim, as detailed in Ezekiel chapter ten.
The cherubim above the ark of the covenant faced one another with their wings stretched above the mercy seat (Exodus 25:18-20). It was there between these majestic angels that God manifested His divine presence. However, Hebrews 9:4 also draws our attention to the items that resided within the ark: “…a gold jar containing manna, Aaron’s rod that budded, and the stone tablets of the covenant” (CEB).
Although this passage summarizes the ark’s contents, it also appears that some items may have been added or deleted over time. For instance, Exodus 25:16 tells us that God directed Moses to “Place inside the Ark the stone tablets inscribed with the terms of the covenant, which I will give to you” (NLT). Later on we’re told, “…Aaron put the manna with the tablets of the covenant law, so that it might be preserved” (Exodus 16:34 NIV). Finally, God gave the following directive to Moses in Numbers 17:10: “‘Put back the staff of Aaron before the testimony…'” (ESV).
But by the time we reach the Old Testament book of 1 Kings, we’re told, “There was nothing in the ark except the two tablets of stone that Moses put there at Horeb, where the Lord made a covenant with the people of Israel, when they came out of the land of Egypt” (1 Kings 8:9 ESV). So it seems that the contents of the ark changed over the course of Israel’s history.
Thus, as one scholar concludes, “Originally, all three items (tables of stone, pot of manna, and Aaron’s rod) were in the ark (as Heb. 9:4 says). Subsequently, the last two were removed (Ex. 40:20).” (1)
(1) Norman L. Geisler and Thomas A. Howe, When Critics Ask : A Popular Handbook on Bible Difficulties (Wheaton, Ill.: Victor Books, 1992), [Hebrews 9:4].