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Decrypt Mendeley


The following article was originally written by Tony Garnock-Jones , which provides steps for .deb versions of Mendeley. I have altered the steps to include Flatpak versions of Mendeley. The original article can be found here.

In an effort to stop users from porting their databases to other software like Zotero, Mendeley has begun encrypting the user database. Mendeley is using the SQLite Encryption Extension (“SEE”) with a hidden key. The SEE library is closed-source and very proprietary. Its API is documented, but its on-disk structures are not (publicly) documented, and the source code is not publicly available. Applications using SEE are required to make it impossible to access SEE functionality from outside the application.


This method is working on Linux (Ubuntu 20.04 and Pop!_OS 20.04).

You will need to install:

  • gdm: sudo apt-get install -y gdm

Mendeley should be installed in either two ways:

  • Flatpak app
  • from a .deb file

Extract your data

  1. Make sure you quit Mendeley before proceeding.
  2. Locate your Mendeley database, the database is usually found in either:

    • ~/.local/share/data/Mendeley\ Ltd./Mendeley\ Desktop/
    • ~/.var/app/com.elsevier.MendeleyDesktop/data/data/Mendeley\ Ltd./Mendeley\ Desktop/

    You will find several sqlite databases:

  3. Make a backup copy of the encrypted database. In my case, I installed Mendeley as a Flatpak app so I ran the following to make a backup copy:

    cd ~/.var/app/com.elsevier.MendeleyDesktop/data/data/Mendeley\ Ltd./Mendeley\ Desktop/
    cp ~/backup-encrypted.sqlite
  4. You will now run Mendeley in debug mode, depending on how you installed it:

    a. if you installed with a .deb package, debug using gdb directly:

    mendeleydesktop --debug

    b. if you installed with Flatpak, you need to run with Flatpak first then gdb:

    # Run with Flatpak
    $ flatpak run --devel --command=sh com.elsevier.MendeleyDesktop
    # Run gdb within the Flatpak sandbox
    [📦 com.elsevier.MendeleyDesktop ~]$ QT_QPA_PLATFORM_PLUGIN_PATH=/app/extra/plugins/qt/plugins/platforms/ gdb --args /app/extra/bin/mendeleydesktop
  5. Add a breakpoint that captures the moment a SQLite database is opened:

    (gdb) b sqlite3_open_v2
  6. Start the program now:

    (gdb) run
  7. The program will stop at the breakpoint several times. Keep continuing the program until the string pointed to by $rdi names the file you backed up in the step above (press c to continue and enter x/s $rdi to check the filename):

    # Run x/s $rdi and look at the filename
    Thread 1 "mendeleydesktop" hit Breakpoint 1, 0x000000000101b1b0 in sqlite3_open_v2 ()
    (gdb) x/s $rdi
    0x1dca928:  "~/.var/app/com.elsevier.MendeleyDesktop/share/data/data/Mendeley Ltd./Mendeley Desktop/Settings.sqlite"
    # Enter c to continue
    (gdb) c
    Thread 1 "mendeleydesktop" hit Breakpoint 1, 0x000000000101b1b0 in sqlite3_open_v2 ()
    (gdb) x/s $rdi
    0x1dcb318:  "~/.var/app/com.elsevier.MendeleyDesktop/share/data/data/Mendeley Ltd./Mendeley Desktop/Settings.sqlite"
    (gdb) c
    # Keep repeating the above until you find the .sqlite file that you backed up earlier
    Thread 1 "mendeleydesktop" hit Breakpoint 1, 0x000000000101b1b0 in sqlite3_open_v2 ()
    (gdb) x/s $rdi
    0x25f1818:  "~/.var/app/com.elsevier.MendeleyDesktop/share/data/data/Mendeley Ltd./Mendeley Desktop/"
  8. You will need to continue (c) until you see the same database filename appear again (x/s $rdi), usually happens immediately after the first appearance.

  9. Now, set a breakpoint for the moment the key is supplied to SQLite Encryption Extension by using b sqlite3_key:

    # Set a new breakpoint
    (gdb) b sqlite3_key
    Breakpoint 2 at 0x101b2c0
    # Press c to continue
    (gdb) c
  10. When the subsequent breakpoint is hit, enter info registers to determine the value of rdi:

    # When the breakpoint is hit, run `info registers`
    Thread 1 "mendeleydesktop" hit Breakpoint 2, 0x000000000101b2c0 in sqlite3_key ()
    (gdb) info registers 
    rax            0x7fffffffc6b0     140737488340656
    rbx            0x25f0590          39781776
    rcx            0x7fffea9a0c40     140737129352256
    rdx            0x20             32
    rsi            0x260fd68          39910760
    rdi            0x25ef4e8          39777512
    rbp            0x7fffffffc730     0x7fffffffc730
    rsp            0x7fffffffc688     0x7fffffffc688
    r8             0xc1             193
    r9             0x7fffea9a0cc0     140737129352384
    r10            0x0              0
    r11            0x1              1
    r12            0x7fffffffc6b0     140737488340656
    r13            0x7fffffffc6a0     140737488340640
    r14            0x7fffffffc790     140737488340880
    r15            0x7fffffffc790     140737488340880
    rip            0x101b2c0          0x101b2c0 <sqlite3_key>
    eflags         0x202              [ IF ]
    cs             0x33             51
    ss             0x2b             43
    ds             0x0              0
    es             0x0              0
    fs             0x0              0
    gs             0x0              0
  11. Copy down the value of rdi from the second column of the info registers output. It is the pointer to the open SQLite database handle. Then, finish execution of sqlite3_key by running fin.

    (gdb) fin
    Run till exit from #0  0x000000000101b2c0 in sqlite3_key ()
    0x0000000000f94e54 in SqliteDatabase::openInternal(QString const&, SqlDatabaseKey*) ()
  12. Use gdb’s ability to call C functions to rekey the database to the null key, thereby decrypting it in-place and allowing export of the SQL data:

    (gdb) p (int) sqlite3_rekey_v2(0x25ef4e8, 0, 0, 0)
    $1 = 0
  13. If you see $1 = 0 from the rekey command then you are ready to export the SQL data (step 14), if you see $1 = 8 then you need to follow the below steps.

    • Mendeley will sometimes re-open the database a few times during startup sp this may have caused the error
    • To work around the random opening of the database, check if the program opens the main database a second time
    • Run step 7-8 again up to the p sqlite3_rekey_v2(...) step, but do not run sqlite3_rekey_v2
    • Instead, just type c to continue, returning to the step where you inspect each call to sqlite3_open_v2, waiting for one with $rdi pointing to a string with the right database filename. When you see it come round again, then try the sqlite3_rekey_v2 step
    • If you see $1 = 0 this time, you’re all set, and can proceed as described above for a successful call to sqlite3_rekey_v2
  14. Once the database is decrypted it is a good idea to save a copy of the database to a new location:

    cd ~/.var/app/com.elsevier.MendeleyDesktop/data/data/Mendeley\ Ltd./Mendeley\ Desktop/
    cp ~/backup-decrypted.sqlite
  15. Now you can quit gbd:

    (gdb) quit
    A debugging session is active.
        Inferior 1 [process 32750] will be killed.
    Quit anyway? (y or n) y
    [322:322:0100/] Invalid node channel message

    if also running Flatpak:

    [📦 com.elsevier.MendeleyDesktop ~]$ exit
  16. Lastly, restore your backup copy of the encrypted database, so that Mendeley will continue to run OK:

    cd ~/.var/app/com.elsevier.MendeleyDesktop/data/data/Mendeley\ Ltd./Mendeley\ Desktop/
    cp ~/backup-encrypted.sqlite
  17. You can now use software like SQLite Browser to open and view the database (~/backup-decrypted.sqlite)