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Microsoft Intune custom compliance lets you evaluate Linux-specific values that built-in checks do not cover. The design uses two coordinated files: a discovery script that runs on the Linux endpoint and emits JSON, and a rules file that tells Intune how to evaluate each returned value. As of August 18, 2026, Microsoft documents support for Ubuntu Desktop 24.04 LTS or 26.04 LTS and Red Hat Enterprise Linux 9 or 10.
The script reports data; the JSON rules determine compliance. A noncompliant result can contribute to the device’s overall Intune state and, where the normal Microsoft Entra, enrollment, assignment and Conditional Access prerequisites are met, access decisions. It does not repair the Linux device.
Requirements and limits
- A supported, enrolled and successfully managed Linux device: Ubuntu Desktop 24.04 LTS or 26.04 LTS, or Red Hat Enterprise Linux 9 or 10. Script execution on another distribution does not make that distribution an Intune-supported platform. See Microsoft’s custom-compliance JSON documentation.
- Intune permissions to upload Linux discovery scripts and create compliance policies, plus a pilot user or device group.
- An interpreter installed and configured on every target device. Microsoft permits any available interpreter; declare it with a shebang such as
#!/bin/bash,#!/bin/shor#!/usr/bin/env python3. - A read-only script that works as the signed-in user. Linux discovery scripts run in that context, so checks requiring root access, such as protected files under
/etc, may fail. Details are in Microsoft’s discovery-script guidance. - One discovery script per policy, up to 100 JSON rules, a rules file no larger than 100 KB, a script no larger than 1 MB, output no larger than 1 MB, and execution within five minutes.
Use custom compliance for a narrow local check, not as a configuration-management or remediation system. Handle fixes with configuration scripts, package management, a management platform or an administrator.
How the two files fit together
The contract is exact and case-sensitive:
Linux device → discovery script → one JSON output object → JSON rules → setting state → overall complianceIf the script prints {"EdgeRunning":true}, the rule must use "SettingName": "EdgeRunning". edgerunning or EdgeStatus is a different setting. Every rule must receive a value on every execution path.
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Build a Linux discovery script
Example Bash script
#!/bin/bash
# Report whether Microsoft Edge is running.
if pgrep -x "msedge" >/dev/null 2>&1; then
edge_running=true
else
edge_running=false
fi
# Standard output must contain only the JSON object.
printf '{"EdgeRunning":%s}n' "$edge_running"
Expected output is {"EdgeRunning":true} or {"EdgeRunning":false}. The variable name is irrelevant; the emitted JSON key is what Intune matches. Send diagnostics to a file or standard error, never into standard output. Quote paths and values, avoid sudo, use portable commands, and test separately on Ubuntu and RHEL.
Test before uploading
chmod +x ./linux-discovery.sh
./linux-discovery.sh
./linux-discovery.sh | python3 -m json.tool
- The command exits successfully.
- Output is one valid JSON object with no logging text.
- Every expected key is present.
- Booleans and numbers are JSON values, not quoted strings.
- The script finishes well below five minutes.
Microsoft’s shell-intune-samples repository includes Linux examples; test samples in a nonproduction ring before deployment.
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Write the JSON rules file
Each rule requires SettingName, Operator, DataType, Operand, MoreInfoUrl and RemediationStrings. Include at least one remediation string with language en_US.
{
"Rules": [
{
"SettingName": "EdgeRunning",
"Operator": "IsEquals",
"DataType": "Boolean",
"Operand": true,
"MoreInfoUrl": "https://example.contoso.com/linux-compliance/edge-running",
"RemediationStrings": [
{
"Language": "en_US",
"Title": "Microsoft Edge must be running.",
"Description": "Start Microsoft Edge and refresh the device compliance status."
}
]
}
]
}
Supported operators are IsEquals, NotEquals, GreaterThan, GreaterEquals, LessThan and LessEquals. Supported data types are Boolean, Int64, Double, String, DateTime and Version. For example:
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| Purpose | DataType | Operand example |
|---|---|---|
| Encryption flag | Boolean | true |
| Package version text | String | "1.2.3" |
| Minimum agent release | Version | "2.3" |
| Update age | Int64 | 14 |
Do not return "true" for a Boolean rule, a number as text for an integer rule, or a locale-dependent date. A syntactically valid rules file can still fail if runtime output is missing, mis-cased or the wrong type. Microsoft’s field and limit reference is here.
Upload the discovery script
- Sign in to the Microsoft Intune admin center.
- Open Endpoint security > Device compliance > Scripts.
- Select Add and choose the Linux platform.
- Enter a name on Basics.
- On Settings, upload the file as the detection (discovery) script.
- Review and complete creation.
These labels were current on August 18, 2026; tenants may show equivalent wording after portal navigation changes. Intune does not validate your script’s syntax or program logic during upload, so a successful upload is not a functional test.
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Create and assign the compliance policy
- Go to Devices > Compliance policies and select Create policy.
- Choose Linux, then provide the policy name and description.
- Configure the built-in Linux settings that also apply.
- Enable or add custom compliance in the configuration settings.
- Select the uploaded discovery script and upload the JSON rules file.
- Configure noncompliance actions, notifications and grace-period behavior required by your organization.
- Assign first to a pilot user or device group.
- Monitor compliance and expand each device to inspect per-setting results.
Version the script and JSON as one unit. Changing a key, type or meaning in only one file creates an avoidable mismatch.
Run a repeatable test plan
- Verify the compliant state and confirm the expected setting appears.
- Intentionally create a noncompliant state and confirm the remediation text.
- Test a missing value, unavailable interpreter, inaccessible path, malformed JSON and wrong data type.
- Test an offline device and then its next successful check-in.
- On Linux, refresh device settings or the compliance issue view in the Microsoft Intune app to trigger a new check according to Microsoft’s troubleshooting guidance.
Troubleshoot common errors
| Code | Meaning | Likely causes and fixes |
|---|---|---|
| 65007 | Script returned failure | Missing interpreter, bad shebang, unavailable command, permissions or timeout. Run as the target user, correct the interpreter, use portable commands and stay under five minutes. |
| 65008 | Setting missing in script result | Case mismatch, typo, conditional omission or early exit. Compare every SettingName with actual output and emit every key on every path. |
| 65009 | Invalid JSON for discovered setting | Debug text, broken quoting, truncation or malformed JSON. Pipe exact output to python3 -m json.tool and keep standard output JSON-only. |
| 65010 | Invalid data type | Quoted Boolean or number, invalid date, or unparsable version. Inspect raw output and synchronize the declared type and emitted value. |
If a policy or script is not visible, refresh the portal; if it remains absent, cancel creation and start again. If a fixed device remains noncompliant, verify the local condition as the same user, refresh the Intune app, inspect issue details, confirm assignment, allow for reporting delay, and temporarily test a simpler rule.
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Production design recommendations
- Keep scripts read-only, deterministic and narrowly scoped.
- Store both files in source control, review changes, record versions and retain a rollback copy.
- Validate shell behavior and command availability on each supported distribution.
- Use stable output schemas; do not silently change names or types.
- Use pilot, staged deployment and monitoring before broad assignment.
- Protect executable code with your organization’s review and integrity controls.
- Choose built-in compliance when it covers the requirement. For root-level configuration, patching and fleet operations, evaluate Canonical Landscape or Red Hat Insights. For threat detection and vulnerability posture, consider Microsoft Defender for Endpoint alongside Intune. These are category alternatives, not automatic replacements.
When this approach fits
Custom compliance is a good fit for a required package, minimum agent version, running process, readable configuration marker, non-root security-tool status or locally calculated age. It is a poor fit for root-only checks, expensive network-dependent calculations, machine modification, broad unsupported-distro coverage or full Linux configuration management.
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