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WSL 3.0.1: binfmt cli handler takes precedence over WSLInterop, breaking Windows executable interop #41739

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WSL 3.0.1: binfmt cli handler takes precedence over WSLInterop, breaking Windows executable interop#41739
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benhillis

Description

@DavidZidar
David Zidar (DavidZidar)
opened on Sep 30, 2026

Windows Version

Microsoft Windows 10.0.26200

WSL Version

3.0.1.0

Are you using WSL 1 or WSL 2?

  • WSL 2
  • WSL 1

Kernel Version

6.18.40.1-microsoft-standard-WSL2

Distro Version

Debian 13 - Though other users have reported the same issue with Ubuntu and Arch as well.

Other Software

Mono

Repro Steps

  • Setup Debian in WSL
  • Install Mono apt install mono-complete
  • Update WSL to 3.0.1
  • Try to run a Windows binary like notepad.exe

Expected Behavior

The binary should run in Windows via WSLInterop.

Actual Behavior

An error message is printed:

run-detectors: unable to find an interpreter for /mnt/c/WINDOWS/system32/notepad.exe

Diagnostic Logs

No response

Workaround/fix

With the help of Copilot I was able to figure out that a registered binfmt_misc handler matching Windows PE executables (MZ) takes precedence over WSLInterop. In my Debian installation this is the cli handler installed by Mono.

Temporary workaround, disable the "cli" handler with:

sudo update-binfmts --disable cli

Permanent workaround, remove the "cli" handler with (thanks joseaporo):

sudo update-binfmts --package mono-runtime --remove cli /usr/bin/cli

Activity

  1. github-actions commented on Sep 30, 2026

    @github-actions
    github-actionsBot
    on Sep 30, 2026 – with GitHub Actions
    Contributor

    Logs are required for review from WSL team

    If this a feature request, please reply with '/feature'. If this is a question, reply with '/question'.
    Otherwise, please attach logs by following the instructions below, your issue will not be reviewed unless they are added. These logs will help us understand what is going on in your machine.

    How to collect WSL logs

    Download and execute collect-wsl-logs.ps1 in an administrative powershell prompt:

    Invoke-WebRequest -UseBasicParsing "https://raw.githubusercontent.com/microsoft/WSL/master/diagnostics/collect-wsl-logs.ps1" -OutFile collect-wsl-logs.ps1
Set-ExecutionPolicy Bypass -Scope Process -Force
.\collect-wsl-logs.ps1

    The script will output the path of the log file once done.

    If this is a networking issue, please use .\collect-wsl-logs.ps1 -LogProfile networking instead, following the instructions in Collect WSL logs for networking issues

    Once completed please upload the output files to this GitHub issue.

    See Collect WSL logs (recommended method).

    If you choose to email these logs instead of attaching them to the bug, please send them to [email protected] with the GitHub issue number in the subject, and include a link to your GitHub issue comment in the message body, and reply with '/emailed-logs'.

  2. github-actions
    added
    needs-author-feedback
    on Sep 30, 2026

  3. DavidZidar commented on Sep 30, 2026

    @DavidZidar
    David Zidar (DavidZidar)
    on Sep 30, 2026
    Author

    I don't see how logs won't be helpful here, I have described the problem.

  4. microsoft-github-policy-service
    removed
    needs-author-feedback
    on Sep 30, 2026

  5. joseaporo commented on Sep 30, 2026

    @joseaporo
    joseaporo
    on Sep 30, 2026

    Same issue here, confirming it is not Debian-specific.

    Environment

    • WSL 3.0.1.0, kernel 6.18.40.1-microsoft-standard-WSL2
    • Ubuntu 24.04, systemd enabled
    • mono-runtime 6.8.0.105+dfsg-3.6ubuntu2 (pulls in binfmt-support 2.2.2-7, which registers the cli handler on magic MZ)

    Regression window
    Interop worked on kernel 6.18.33.2 and broke on the first boot after the auto-update to 3.0.1. Mono and binfmt-support were installed months earlier and unchanged.

    Likely cause: #40621 ("protect binfmt_misc from cross-distro wipe at shutdown"). It first shipped in prerelease 2.9.3; comparing tags shows it is in 3.0.1 but not in 2.7.14, so stable users are seeing it for the first time.

    Boot journal comparison on the same machine:

    • Every boot before the update logged this from init, after systemd-binfmt ran:
      sh: 1: cannot create /proc/sys/fs/binfmt_misc/WSLInterop: Permission denied
    • Every boot after the update no longer shows that line, and instead shows:
      systemd-binfmt: Failed to flush binfmt_misc rules, ignoring: Read-only file system

    So the old flow appears to have been: systemd flushed the registry, then WSLInterop was registered again last and won. With /status now read-only, the flush fails, WSLInterop is registered early, and binfmt-support.service (ExecStart=update-binfmts --enable) registers cli after it. The most recently registered matching entry wins, so cli intercepts every PE file.

    Workaround notes

    • sudo update-binfmts --disable cli works but does not survive a restart; binfmt-support.service enables cli again on the next boot.
    • Lasting workaround: sudo update-binfmts --package mono-runtime --remove cli /usr/bin/cli (what the mono-runtime prerm runs on uninstall). A mono-runtime upgrade can register it again.

    Any distro with binfmt-support plus a package that registers an MZ handler (mono, wine) is likely affected. WSLInterop should probably keep precedence over distro-registered MZ handlers now that the flush no longer happens.

  6. DavidZidar commented on Sep 30, 2026

    @DavidZidar
    David Zidar (DavidZidar)
    on Sep 30, 2026
    Author

    Nice analysis, thanks! I can confirm that my workaround did not survive a restart and have updated the issue description.

  7. OneBlue commented on Sep 30, 2026

    @OneBlue
    Blue (OneBlue)
    on Sep 30, 2026
    Collaborator

    /logs

  8. microsoft-github-policy-service commented on Sep 30, 2026

    @microsoft-github-policy-service
    microsoft-github-policy-serviceBot
    on Sep 30, 2026 – with Microsoft GitHub Policy Service
    Contributor

    Hello! Could you please provide more logs to help us better diagnose your issue?

    To collect WSL logs, download and execute collect-wsl-logs.ps1 in an administrative powershell prompt:

    Invoke-WebRequest -UseBasicParsing "https://raw.githubusercontent.com/microsoft/WSL/master/diagnostics/collect-wsl-logs.ps1" -OutFile collect-wsl-logs.ps1
Set-ExecutionPolicy Bypass -Scope Process -Force
.\collect-wsl-logs.ps1

    The script will output the path of the log file once done.

    Once completed please upload the output files to this GitHub issue.

    See Collect WSL logs (recommended method).

    If you choose to email these logs instead of attaching them to the bug, please send them to [email protected] with the GitHub issue number in the subject, and include a link to your GitHub issue comment in the message body.

    Thank you!

  9. microsoft-github-policy-service
    added
    needs-author-feedback
    on Sep 30, 2026

  10. joseaporo commented on Sep 30, 2026

    @joseaporo
    joseaporo
    on Sep 30, 2026

    /emailed-logs

  11. julianxhokaxhiu commented on Sep 30, 2026

    @julianxhokaxhiu
    Julian Xhokaxhiu (julianxhokaxhiu)
    on Sep 30, 2026

    Same issue here on Arch

    ❯ systemctl status systemd-binfmt.service
× systemd-binfmt.service - Set Up Additional Binary Formats
     Loaded: loaded (/usr/lib/systemd/system/systemd-binfmt.service; static)
     Active: failed (Result: exit-code) since Wed 2026-09-30 22:59:01 CEST; 3s ago
 Invocation: d122c0f34f70473997f796388570412f
       Docs: man:systemd-binfmt.service(8)
             man:binfmt.d(5)
             https://docs.kernel.org/admin-guide/binfmt-misc.html
             https://systemd.io/API_FILE_SYSTEMS
    Process: 1149 ExecStart=/usr/lib/systemd/systemd-binfmt (code=exited, status=1/FAILURE)
   Main PID: 1149 (code=exited, status=1/FAILURE)
   Mem peak: 4.4M
        CPU: 7ms

Sep 30 22:59:01 PC-FISSO systemd[1]: Starting Set Up Additional Binary Formats...
Sep 30 22:59:01 PC-FISSO systemd-binfmt[1149]: Failed to flush binfmt_misc rules, ignoring: Read-only file system
Sep 30 22:59:01 PC-FISSO systemd[1]: systemd-binfmt.service: Main process exited, code=exited, status=1/FAILURE
Sep 30 22:59:01 PC-FISSO systemd[1]: systemd-binfmt.service: Failed with result 'exit-code'.
Sep 30 22:59:01 PC-FISSO systemd[1]: Failed to start Set Up Additional Binary Formats.

    WSL info

    ❯ wsl --version
Versione WSL: 3.0.1.0
Versione kernel: 6.18.40.1-1
Versione WSLg: 1.0.79
Versione MSRDC: 1.2.7214
Versione Direct3D: 1.611.1-81528511
Versione DXCore: 10.0.26100.1-240331-1435.ge-release
Versione di Windows: 10.0.26300.9550
  12. David Zidar (DavidZidar)
    changed the title [-]WSL 3.0.1: Debian binfmt cli handler takes precedence over WSLInterop, breaking Windows executable interop[/-] [+]WSL 3.0.1: binfmt cli handler takes precedence over WSLInterop, breaking Windows executable interop[/+] on Oct 1, 2026

  13. github-actions commented on Oct 1, 2026

    @github-actions
    github-actionsBot
    on Oct 1, 2026 – with GitHub Actions
    Contributor

    Logs are required for review from WSL team

    If this a feature request, please reply with '/feature'. If this is a question, reply with '/question'.
    Otherwise, please attach logs by following the instructions below, your issue will not be reviewed unless they are added. These logs will help us understand what is going on in your machine.

    How to collect WSL logs

    Download and execute collect-wsl-logs.ps1 in an administrative powershell prompt:

    Invoke-WebRequest -UseBasicParsing "https://raw.githubusercontent.com/microsoft/WSL/master/diagnostics/collect-wsl-logs.ps1" -OutFile collect-wsl-logs.ps1
Set-ExecutionPolicy Bypass -Scope Process -Force
.\collect-wsl-logs.ps1

    The script will output the path of the log file once done.

    If this is a networking issue, please use .\collect-wsl-logs.ps1 -LogProfile networking instead, following the instructions in Collect WSL logs for networking issues

    Once completed please upload the output files to this GitHub issue.

    See Collect WSL logs (recommended method).

    If you choose to email these logs instead of attaching them to the bug, please send them to [email protected] with the GitHub issue number in the subject, and include a link to your GitHub issue comment in the message body, and reply with '/emailed-logs'.

  14. DavidZidar commented on Oct 1, 2026

    @DavidZidar
    David Zidar (DavidZidar)
    on Oct 1, 2026
    Author

    Logs have been provided by joseaporo. I just updated the issue to make it clear that is is not Debian specific.

  15. microsoft-github-policy-service
    removed
    needs-author-feedback
    on Oct 1, 2026
  16. Blue (OneBlue)
    assigned
    Ben Hillis (benhillis)
    on Oct 1, 2026

  17. julianxhokaxhiu commented on Oct 5, 2026

    @julianxhokaxhiu
    Julian Xhokaxhiu (julianxhokaxhiu)
    on Oct 5, 2026

    Just wanted to let you know that I tested the 3.0.2 prebuilt binary (available here https://dev.azure.com/shine-oss/wsl/_build/results?buildId=390175&view=artifacts&pathAsName=false&type=publishedArtifacts ) and I've found something curious.

    While the fix for binfmt works and I can run now binaries like code to open VSCode from WSL, the systemd status still is flagged as degraded.

    Reporting the technical info for you to eventually figure out a solution:

    Arch (WSL)

    ❯ ls /proc/sys/fs/binfmt_misc
CLR  register  status  WSLInterop
❯ cat /proc/sys/fs/binfmt_misc/status
enabled
❯ cat /proc/sys/fs/binfmt_misc/CLR
enabled
interpreter /usr/bin/mono
flags:
offset 0
magic 4d5a
❯ cat /proc/sys/fs/binfmt_misc/WSLInterop
enabled
interpreter /init
flags: PF
offset 0
magic 4d5a
❯ systemctl --failed
  UNIT                   LOAD   ACTIVE SUB    DESCRIPTION
● systemd-binfmt.service loaded failed failed Set Up Additional Binary Formats

Legend: LOAD   → Reflects whether the unit definition was properly loaded.
        ACTIVE → The high-level unit activation state, i.e. generalization of SUB.
        SUB    → The low-level unit activation state, values depend on unit type.

1 loaded units listed.

~ on  master
❯ systemctl status systemd-binfmt.service
× systemd-binfmt.service - Set Up Additional Binary Formats
     Loaded: loaded (/usr/lib/systemd/system/systemd-binfmt.service; static)
    Drop-In: /run/systemd/generator/systemd-binfmt.service.d
             └─override.conf
     Active: failed (Result: exit-code) since Mon 2026-10-05 23:13:23 CEST; 1min 10s ago
 Invocation: 3e86a3c721a74abf8adce2704613004a
       Docs: man:systemd-binfmt.service(8)
             man:binfmt.d(5)
             https://docs.kernel.org/admin-guide/binfmt-misc.html
             https://systemd.io/API_FILE_SYSTEMS
   Main PID: 151 (code=exited, status=1/FAILURE)
   Mem peak: 2.3M
        CPU: 12ms

Oct 05 23:13:23 PC-FISSO systemd[1]: Starting Set Up Additional Binary Formats...
Oct 05 23:13:23 PC-FISSO systemd-binfmt[151]: Failed to flush binfmt_misc rules, ignoring: Read-only file system
Oct 05 23:13:23 PC-FISSO systemd[1]: systemd-binfmt.service: Main process exited, code=exited, status=1/FAILURE
Oct 05 23:13:23 PC-FISSO systemd[1]: systemd-binfmt.service: Failed with result 'exit-code'.
Oct 05 23:13:23 PC-FISSO systemd[1]: Failed to start Set Up Additional Binary Formats.

    WSL

    ❯ wsl --version
Versione WSL: 3.0.2.0
Versione kernel: 6.18.40.1-1
Versione WSLg: 1.0.79
Versione MSRDC: 1.2.7391
Versione Direct3D: 1.611.1-81528511
Versione DXCore: 10.0.26100.1-240331-1435.ge-release
Versione di Windows: 10.0.26300.9550
Versione di MSBuild: 1944
Commit: 0dc1bc1f
Tempo di compilazione: 00:19:12 Oct  3 2026

    I wonder if the issue is because once you define the binfmt_misc file-system entry point you mark it also as read-only so anything else inside the container can't override it. Wouldn't be much simpler if you define your own custom unit and you make it dependant on systemd-binfmt.service and you register it forcefully on some well-known paths in /var/lib/systemd for eg. so you can generate it as read-only yet systemd picks it up and runs it as a normal unit? Just suggesting ideas as the solution "works" but is not yet in its optimal shape.

    Hope this helps, thanks a lot nevertheless for working on it!

  18. OneBlue commented on Oct 5, 2026

    @OneBlue
    Blue (OneBlue)
    on Oct 5, 2026
    Collaborator

    Fixed by 3.0.2

    There is a remaining issue causing the binfmt unit to get into a failed state, but let's track that as a separate issue

  19. Blue (OneBlue)
    closed this as completedon Oct 5, 2026
  20. Zoltan Csizmadia (zcsizmadia)
    added a commit that references this issue on Oct 25, 2026

    doctor: KVM001, BIN001 and NET005 from the WSL 3.0.x issues (#121)

    b1c2524
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