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Comparing Intune scripting methods: native scripting with scattered blocks and random arrows representing asynchronous execution risks vs. 'Orchestrated Sequences' with a vertical stack of steps connected by a single downward arrow representing a forced, logical order of operations.

NERDIO GUIDE

Intune script deployment best practices

Carisa Stringer | January 28, 2026

Introduction

Intune script deployment is a critical method for automating device configuration and management across Windows, macOS, and Linux endpoints. By using scripts, you can execute complex administrative tasks that go beyond the standard configuration profiles available in Microsoft Intune. 

Mastering these deployment practices ensures your environment remains secure, compliant, and standardized without requiring manual intervention on every device.

What is Intune script deployment and when should I use it?

Microsoft Intune uses the Intune Management Extension (IME) to execute scripts on managed devices, filling the gap where native MDM policies might fall short. Understanding the distinction between a script and a Win32 app is essential for choosing the right tool for your specific administrative task.

When should I use a script instead of a Win32 app?

While both can execute code, they serve different primary functions. You should use scripts for lightweight, "fire-and-forget" configurations, while Win32 apps are better suited for complex software installations.

  • Use Scripts for: Mapping network drives, modifying registry keys, removing bloatware, or running one-time configuration checks. Beyond basic settings, you can also use scripts to proactively uninstall unauthorized applications or remove persistent bloatware that standard MDM policies cannot reach.
  • Use Win32 Apps for: Software that requires a detection rule, complex dependencies, or large installation files.

What are the main benefits of using PowerShell scripts in Intune?

PowerShell is the standard for Windows automation, allowing you to interface directly with the OS. It provides granular control over system settings that are not yet exposed in the Intune Settings Catalog. According to Microsoft, scripts allow for a highly customizable management experience, especially during the Initial Device Setup (Autopilot) phase. When a script is assigned, the Intune Management Extension serves as the client-side agent that checks for new assignments every 60 minutes to ensure the Windows device remains in sync with the latest configurations.

How do I prepare PowerShell scripts for Intune deployment?

Preparing your scripts correctly is the difference between a seamless rollout and a wave of helpdesk tickets. You must consider the security context and the architecture of the host machine to ensure the script executes as intended.

Should I run my Intune script in the system or user context?

The execution context determines what permissions the script has and which part of the registry it can access. Choosing the wrong context is a leading cause of script failure during deployment.

  • System Context: Use this for administrative changes like installing drivers, modifying HKEY_LOCAL_MACHINE (HKLM), or managing system services.
  • User Context: Use this for user-specific settings such as mapping a drive to a user's profile, modifying HKEY_CURRENT_USER (HKCU), or creating desktop shortcuts.

Why should I use the 64-bit PowerShell host in Intune?

By default, Intune may attempt to run scripts in a 32-bit (x86) context, which can lead to "Registry Reflection" issues where changes are redirected to SysWOW64 instead of the intended system folders.

Best Practice: Always toggle the "Run script in 64-bit PowerShell host" to Yes unless you specifically need to interact with a 32-bit application. This ensures your script interacts with the modern 64-bit architecture found on most enterprise devices running Windows 10 or Windows 11 today.

What are the best practices for logging and monitoring Intune scripts?

Visibility is the most significant challenge in script management, as errors often occur silently when pushing updates to users. Without robust logging, you cannot verify compliance or troubleshoot why a deployment failed on a specific subset of devices.

How do I get better visibility into script execution failures?

Native Intune reporting is often delayed and only provides a basic "Success" or "Failure" status. To gain deeper insight, you should implement local logging within your PowerShell scripts. While standard tools offer a limited view of your deployment's health, enterprise-grade orchestration provides a "glass box" approach to management. This level of detail is a significant upgrade over native binary feedback, providing the deep visibility found in advanced reporting for Microsoft Intune to ensure administrators can verify compliance and performance across the entire fleet.

The following comparison highlights the "visibility gap" between binary reporting and granular, step-by-step logging.

Comparing a 'Black Box' native Intune reporting side with a single success/fail status versus a 'Glass Box' enterprise orchestration side showing a granular, step-by-step checklist of script execution milestones with real-time logs

Let’s walk through the diagram above…

Native "Black Box" Reporting: Standard Intune deployment provides only a final status. If a script fails, IT admins are left "flying blind" without knowing exactly where it stopped.

Sequential "Glass Box" Visibility: Orchestration through Nerdio Scripted Sequences breaks the deployment into individual, trackable nodes.

Real-Time Failure Identification: By seeing exactly which step failed—such as a pre-check or a specific registry tweak—you can identify and remediate the root cause immediately rather than manually collecting device logs.

Contextualized Failure Data: Instead of a generic failure message, granular logging shows you exactly which environmental factor or prerequisite check caused a script to halt.

Best Practices for Optimizing Script Reporting

To move away from "binary feedback" and toward granular visibility, your script architecture must include these three elements:

  • Implement Local Transcripts: Include Start-Transcript at the beginning of your PowerShell scripts to record all output to a local folder (e.g., C:\ProgramData\Management\Logs). This creates a "paper trail" on the device that can be harvested if a sequence fails.
  • Structured Error Handling: Use Try-Catch blocks to capture specific exceptions. Instead of the script just "stopping," a Catch block allows you to write the exact error message to your log file before the script exits, making the "where and why" of a failure immediately apparent.
  • Standardized Exit Codes: Ensure your script explicitly returns a 0 for success and a unique non-zero integer for specific failure types. When used with an orchestrator like Nerdio, these codes can trigger automated remediation or specific alerts in the dashboard.

How should I target and schedule script assignments?

Effective targeting ensures that your scripts reach the right devices without causing performance degradation or user interruptions. Proper scheduling and filtering are key components of a stable endpoint management strategy.

Should I use filters or dynamic groups for script targeting?

While both work, Microsoft recommends using Filters for script assignments whenever possible. Filters are evaluated at the time the device checks in, making them significantly faster and more accurate than dynamic groups, which can take hours to update.

How do I handle script scheduling and re-runs?

Standard Intune scripts are designed to run once; they do not natively support recurring schedules without manual intervention.

  • To run a script again: You must change the version or modify the script file in the Intune portal to trigger a re-evaluation.
  • For recurring tasks: Use Microsoft Intune Remediation (formerly Proactive Remediations). This allows you to set a "Detection" script to check for a condition and a "Remediation" script to fix it on a daily or hourly schedule.
Standard Scripts Intune Remediations
Execution Runs once Recurring schedule
Visibility Low (Success/Fail) High (Detection/Remediation state)
Best For One-time configs Compliance & Drift control

Can I create task sequences or dependencies with Intune scripts?

A common frustration for IT admins transitioning from SCCM to Intune is the lack of native task sequences. In a standard Intune environment, scripts run asynchronously, meaning you cannot easily guarantee that "Script A" finishes before "Script B" begins.

What are the risks of pushing scripts without sequencing?

When you push multiple updates or configurations simultaneously, they can conflict, leading to "race conditions." For example, if a script attempts to configure a piece of software before the installation script has finished, both actions may fail, leaving the device in a non-compliant state.

The visual below illustrates the 'race condition' risk of native, asynchronous scripting compared to the predictable success of orchestrated sequences.

The visual illustrates the 'race condition' risk of native, asynchronous scripting compared to the predictable success of orchestrated sequences.

How orchestration solves the sequencing gap

Guaranteed Order of Operations: Unlike native Intune, which triggers scripts simultaneously, orchestration ensures that "Step 2" never begins until "Step 1" confirms a successful exit code. 

Eliminating Race Conditions: By enforcing a strict path, you prevent common conflicts where a configuration script tries to run before the application it’s targeting has finished installing. 

Modular Management: Instead of building "monolithic scripts"—giant, hard-to-maintain files that handle everything at once—you can chain smaller, reusable scripts into a single logical flow. 

Integrated Reboot Handling: Orchestration allows you to programmatically handle reboots between steps, ensuring the device is in the correct state for the next phase of the sequence without breaking the deployment.

How do IT pros typically handle script dependencies?

Without third-party orchestration, admins often resort to "monolithic scripts"—combining many different tasks into one giant PowerShell file. This is difficult to maintain and troubleshoot. Another common workaround is using Win32 app "Dependencies," though this adds significant administrative overhead for simple configuration tasks.

How does Nerdio Manager for Enterprise help with Intune script deployment?

Nerdio Manager for Enterprise provides the orchestration and visibility layer that is often missing in native Intune environments. By extending the core capabilities of the Microsoft Intune platform, Nerdio empowers administrators to handle complex automation scenarios that native tools alone cannot address. It allows IT professionals to move away from fragmented, one-off scripts toward reliable, automated workflows.

How do Scripted Sequences solve the visibility problem?

One of the primary causes of deployment errors is a lack of insight into the device state during an update. Nerdio’s Scripted Sequences allow you to chain together multiple scripts, applications, and even reboots into a single, logical flow.

  • Step-by-Step Visibility: Unlike the "black hole" of native script reporting, Nerdio provides real-time logs for every step in a sequence. You can see exactly which part of the process failed—whether it was a prerequisite check, an app install, or a final registry tweak. This granular logging is also a critical component for delivering accurate cross-tenant AVD and Intune analytics, enabling IT teams to visualize deployment health across multiple identity silos from a single dashboard.

Can Nerdio automate complex deployment tasks?

Nerdio enhances the deployment process by integrating with your existing repositories, such as GitHub or Azure DevOps. This allows for:

  • Version Control: Ensure you are always deploying the latest version of a script without manual uploads.
  • Compliance Checks: Automatically verify that a device meets specific criteria before a script sequence is allowed to run, drastically reducing the error rate during mass updates. These pre-execution validations offer a level of precision that surpasses basic mobile device management protocols, ensuring that scripts only execute when the device environment is perfectly primed.
  • Integrated Reboots: You can programmatically handle reboots within a sequence, ensuring that the device is ready for the next step of the configuration without user intervention.

By using Nerdio to manage these sequences, IT teams gain the "Task Sequence" power of SCCM with the cloud-native flexibility of Microsoft Intune, ensuring that every deployment is predictable, visible, and successful. This seamless orchestration is the cornerstone of a modern unified endpoint management strategy, harmonizing the administration of physical endpoints, Windows 365 management strategies, and Cloud PCs under one robust methodology.


Frequently asked questions


About the author

Photo of Carisa Stinger

Carisa Stringer

Head of Product Marketing

Carisa Stringer is the Head of Product Marketing at Nerdio, where she leads the strategy and execution of go-to-market plans for the company’s enterprise and managed service provider solutions. She joined Nerdio in 2025, bringing 20+ years of experience in end user computing, desktops-as-a-service, and Microsoft technologies. Prior to her current role, Carisa held key product marketing positions at Citrix and Anthology, where she contributed to innovative go-to-market initiatives. Her career reflects a strong track record in driving growth and adoption in the enterprise technology sector. Carisa holds a Bachelor of Science in Industrial Engineering from the Georgia Institute of Technology.

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