Partitions are enabled to be merged in storage device of distributed database systems. A request to merge a plurality of source partitions into a merged partition is received. Each source partition stores a plurality of data items having corresponding source global identifiers and corresponding source local identifiers. The data items, with corresponding metadata, are appended from the source partitions to an intermediate storage structure in an order defined by the source local identifiers. Target global identifiers and target local identifiers are generated for each of the data items in the intermediate storage structure. The copied data items are flushed from the intermediate storage structure to the merged partition in an order defined by the target global identifiers. The source partitions and intermediate storage structure may then be purged of data, removed, and/or reused for further storage needs.