The fee estimation in Bitcoin Core is based on the previous blocks. Since the minimum pruning size for pruned nodes is 550 MB, a pruned node may actually not have the last 1,000 blocks, which is the largest fee estimation interval. Can a pruned node perform its own fee estimation? Does it only have estimates for smaller block targets when it has less history?

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Yes, if it has a mempool (no -blocksonly).

No matter the number of blocks stored, what matters is how many blocks it has been watching (ie received at the time of generation, with transactions that were part of its mempool).

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