In order to attempt an answer, we need to read several passages that speak of the ark.

1) It is clear from Exodus 40:20 and Deuteronomy 10:5 that Moses only put THE TABLETS IN THE ARK. Those verses read: “He (Moses) took the Testimony (the tablets) and put it into the ark, inserted the poles through the rings of the ark, and put the mercy seat on top of the ark….Then I turned and came down from the mountain, and put THE TABLETS IN THE ARK which I had made; and THERE THEY ARE, just as the LORD commanded me.” These verses coincide with 2nd Chronicles 5:10, “Nothing was IN THE ARK EXCEPT THE TWO TABLETS which Moses put there at Horeb.”

2) Now let’s read two passages which speak of the manna and the rod and their connection to the ark. In Exodus 16:33-34 we read, “And Moses said to Aaron, ‘Take a pot and put an omer of MANNA IN IT, and lay it up BEFORE THE LORD, to be kept for your generations.’ As the LORD commanded Moses, so Aaron LAID IT UP BEFORE THE TESTIMONY, to be kept.” Now let’s read Numbers 17:8 & 10-11, “Now it came to pass on the next day that Moses went into the tabernacle of witness, and behold, the ROD OF AARON, of the house of Levi, had sprouted and put forth buds, had produced blossoms and yielded ripe almonds…And the LORD said to Moses, ‘Bring Aaron’s rod back BEFORE THE TESTIMONY, to be kept as a sign against the rebels, that you may put their complaints away from Me, lest they die.’ Thus did Moses; just as the LORD had commanded him, so he did.”

3) Finally, let’s read Hebrews 9:4, “Which had the golden censer and the ark of the covenant overlaid on all sides with gold, in which were the GOLDEN POT THAT HAD THE MANNA, AARON’S ROD that budded, and THE TABLETS OF THE COVENANT.”

The only way to reconcile these passages of Scripture is to see that INITIALLY the ark only contained THE TABLETS (i.e. the Ten Commandments written on stones). Later THE MANNA and THE ROD were added to the ark. Moses put the tablets in as soon as he “came down from the mountain.” Later, Moses had Aaron put the manna in. And finally, Moses added Aaron’s rod to the ark after it had sprouted. These three items remained in the ark for some time while the children of Israel journeyed to the promised land, but once the Temple was built in the land of Palestine, the manna and the rod aren’t mentioned; only the tablets of stone. This Temple is the subject of 2nd Chronicles 5:1-10 which took place in the days of Solomon. The reason Hebrews 9:4 mentions all three items (the manna, the rod and the tablets) is because the subject there is the Tabernacle (which was in the wilderness) and not the Temple (which was built in the Land) and all three items were in the Tabernacle during part of the wilderness journey.

But we still haven’t answered your question: What happened to the manna and the rod? Why weren’t they put into the ark along with the tablets when the Temple was built? Did they disappear somehow or did God simply command Solomon to omit them for some reason? We may never know the answer to this question (at least on this side of glory), but there is an interesting note that should be made. I’m thinking of the significance of the manna and the rod to those who were traveling to the Promised Land. The manna was a reminder to them of God’s FAITHFULNESS AND CARE in feeding them all along the way. The rod was, as we saw in Numbers 10:10, “a sign against the rebels, that you may put their complaints away from Me, lest they die,” so it was a reminder to them of God’s HOLINESS and how he must punish those who rebel against Him. So, the manna and the rod were especially fitting to them, and would not have had that same meaning to the Israelites living in Solomon’s day.  (430.3)  (DO)