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Integrity is maintained by keeping a [[transaction log]] of all changes made to metadata over a certain period of time.<ref name="Forensics" /> The log is written to disk first into free space and then meta data blocks are overwritten directly. Should the system crash, the next time the filesystem is mounted it will notice the uncompleted operation and roll it back to the last known consistent state. For performance reasons, only metadata integrity is ensured. Actual data in files can still be corrupted if a write operation is terminated halfway through.<ref>{{cite web |url=http://www.amiga-stuff.com/text/filesystems/SFS.guide |author=Hendrikx, J |title=Smart Filesystem documentation |date=4 August 1998 |archive-url=https://web.archive.org/web/20040707174441/http://www.amiga-stuff.com/text/filesystems/SFS.guide |archivedate=2004-07-07 }}</ref> Unlike the original Amiga filesystems, [[Amiga Fast File System|FFS]] and [[Amiga Old File System|OFS]], filesystem integrity is very rarely compromised by this.
One feature of SFS that is almost unique among Amiga filesystems is its ability to [[defragmentation|defragment]] itself while the filesystem is in use, even for locked files.<ref name="Forensics" /> The defragmentation process is almost completely stateless (apart from the ___location it is working on), which means it can be stopped and started instantly. During defragmentation data integrity is ensured of both meta data and normal data. The filesystem may attempt to move a whole file to a different ___location when fragmentation is going to occur otherwise.<ref name="Forensics2">{{cite book|author1=Husrev Taha Sencar|author2=
The filesystem offers a directory containing deleted files for recovery.<ref name="TotalAmiga" />
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