How to fix SQLITE_CORRUPT: The database disk image is malformed in SQLite

First, verify the corruption is real by running the integrity check command:

sqlite3 mydb.sqlite3 "PRAGMA integrity_check;"

A healthy database returns "ok". A corrupt database lists specific errors like:
- corruption detected in the index "sqlite_autoindex_table_name"
- missing pages referenced by index
- malformed database record

If the database opens and returns "ok", the problem may be transient or application-specific.

Never attempt recovery without a backup. The original file may help diagnose the issue:

cp mydb.sqlite3 mydb.sqlite3.backup

Keep this backup safe in case recovery goes wrong or you need to investigate further.

SQLite 3.38.0+ includes a dedicated .recover tool for damaged databases:

sqlite3 mydb.sqlite3 ".recover --ignore-freelist" | sqlite3 mydb_recovered.sqlite3

Or for older SQLite versions, use .dump:

echo ".dump" | sqlite3 mydb.sqlite3 > dump.sql

This exports all recoverable data to SQL statements. The .recover method is preferred as it skips unusable free space and doesn't try to restore invalid transaction states.

After the command completes, check the new database:

sqlite3 mydb_recovered.sqlite3 "PRAGMA integrity_check;"

If "ok" is returned, your data is recovered. Replace the original:

mv mydb.sqlite3 mydb.sqlite3.corrupted
mv mydb_recovered.sqlite3 mydb.sqlite3

If the .recover method produces an incomplete or unusable database:

# Export what can be salvaged
sqlite3 mydb.sqlite3 ".mode insert" ".dump" > dump.sql

# Manually edit dump.sql to remove transaction statements if needed:
# - Remove lines starting with "BEGIN TRANSACTION;" and "COMMIT;"
# - Some dumps include invalid data; comment out problematic INSERT statements

# Create fresh database from cleaned dump
sqlite3 mydb_rebuilt.sqlite3 < dump.sql

# Verify integrity
sqlite3 mydb_rebuilt.sqlite3 "PRAGMA integrity_check;"

This method may lose some data but recovers what is structurally valid. Review the SQL dump before importing to catch issues.

Corruption does not happen randomly. Determine the cause to prevent recurrence:

Hardware Issues:

# Check disk health (Linux)
sudo smartctl -a /dev/sda | grep -i "health|fail|error"

# On macOS
diskutil verifyVolume /Volumes/YourDrive

If the disk is failing, replace it and restore from backup.

Concurrent Access Issues:

# Find processes accessing the database
lsof | grep mydb.sqlite3

# Verify only one application has the file open at a time

Application Bugs:
- Review recent code changes that modify the database
- Check application logs for crashes during write operations
- Ensure proper error handling and transaction rollback

Backup/Restore Issues:
- Never backup a database file while it's open in the application
- Stop the application, backup, then restart
- Include the journal file in backups (if using WAL mode)

If you have a recent uncorrupted backup:

cp /path/to/backup/mydb.sqlite3 mydb.sqlite3
sqlite3 mydb.sqlite3 "PRAGMA integrity_check;"

This is the most reliable recovery method. Regular backups are essential for SQLite.