An example method of handling, at a hypervisor on a host in a virtualized computing system, a write input/output (IO) operation to a file on a storage device having a virtual machine file system (VMFS) is described. The method includes: sorting, at the hypervisor, a scatter-gather array for the write IO operation into sets of scatter-gather elements, each of the sets including at least one scatter-gather element targeting a common file block address; resolving offsets of the sets of scatter-gather elements to identify a first scatter-gather array of transaction-dependent scatter-gather elements; generating logical transactions for the first scatter-gather array having updates to metadata of the VMFS for the file; batching the logical transactions into a physical transaction; and executing the physical transaction to commit the updates to the metadata of the VMFS on the storage device for the file.