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The recommended method for storing metadata concerning a collection in Firestore is to create a separate document for the metadata and store it in a subcollection with a specific name like __metadata__. This way, the metadata document and the subcollection can be easily identified and managed separately from the other documents in the collection. Additionally, this approach allows for easy querying and indexing of the metadata document, as well as the ability to add and remove metadata fields without affecting the data in the main collection.