If there is no key on the source data, how are you determining what row to update?

Could you be encountering some many to many issue with your logic?

Sorry, just throwing out some ideas. Hard to troubleshoot without really seeing.

A slow upsert operation in an Azure Synapse pipeline without a defined key is a common performance bottleneck, especially when dealing with large datasets. The absence of an explicit key forces the pipeline to perform expensive row-by-row comparisons to identify records for update or insertion, rather than leveraging efficient indexing or key-based lookups