Configure Sophos Endpoint Application Control

Application Control is intended to stop unwanted or risky software without prematurely treating every unknown application as malware. Sophos assigns known programs to application categories. The policy then decides which ones are allowed or blocked.

The safe starting point is therefore not “block everything unnecessary”, but detect, assess, pilot and only then block. This makes remote-management, administration and collaboration tools that are genuinely used visible before a production block interrupts business processes.

Application Control is not malware protection

Threat Protection detects malicious files and behaviour. Application Control enforces an operational decision for otherwise known applications. A remote-administration tool may be legitimate for support and undesirable on a normal workstation. No blanket default switch can replace this assessment.

Allowing an application in Application Control also does not stop Sophos checking it for malware, exploits, ransomware or malicious behaviour. Conversely, a genuine false positive should not be concealed by a broad Application Control exception.

Detect first

Sign in to Sophos Fusion, then create or open an Application Control policy under My Products > Endpoint > Policies. The policy must be turned on in the Settings tab. Sophos recommends this inventory workflow:

Under Controlled Applications, click Add/Edit List.
Open a relevant category, initially choose Select all applications, and click Save to List. Repeat this for every category you want to inventory.
Under Detection Options, select only Detect controlled applications during scheduled and on-demand scans. Application Control uses the scheduled scans and file types configured in Threat Protection.
Allow every computer to complete at least one scheduled scan.
Go to Reports > Logs > Events, clear every event type except Application Control, and assess the detected applications.

The application name is not the only important value: device, user, time and business purpose also matter. An application that is legitimate on an IT administration device may be unwanted on every other endpoint.

Categories and individual applications

Sophos organises controllable programs into categories. Blocking an entire category is convenient but has a wider impact. Where products in the same category require different treatment, open the category and refine the decision at application level.

A maintainable model typically consists of a few decisions:

Decision	Suitable for
allow category	established software class with clear approval
block category	software class generally prohibited in the organisation
block individual application	exception within an otherwise allowed category
allow individual application	approved product within an otherwise blocked category

Do not fill the policy with many precautionary individual exceptions. Every deviation needs an owner and a traceable reason.

Do not treat Protected Browser and Island Browser separately

Sophos Protected Browser and Island Enterprise Browser currently share core binaries, so Sophos Endpoint can detect both with the same signature. An Application Control decision for Island Browser may therefore also affect Sophos Protected Browser; reliable separate approval is not guaranteed. The overlap also affects DLP browser detection. When using Workspace Protection, test Application Control together with Endpoint DLP and document the product boundary.

Block a pilot group

After reviewing the results, open Add/Edit List again. Clear the checkbox for every application that must remain available; all other entries remain controlled. Then turn on Detect controlled applications when users access them and Block the detected application under Detection Options, and save the policy.

Assign the first blocking policy to a small computer group. It must include typical users, important business applications and at least one IT workstation. After assignment, check Policies on the device to confirm that this Application Control policy is actually effective.

During the pilot, verify:

the expected application is blocked and generates an Event
allowed applications continue to start
Windows users receive the configured desktop message
the helpdesk knows the application, rule and approval process
bypass attempts using portable or renamed programs are detected

Desktop Messaging is on by default. A custom message supplements the standard message; if the field is empty, users see only the standard message. According to Sophos, this feature can only be customised or turned off for Windows computers. On other platforms, the operating process must therefore not depend on users seeing the same dialogue.

Block script hosts only after inventory

Under Programming / Scripting tool, Application Control can control applications such as Microsoft WSH WScript. This adds a barrier against malicious JavaScript files but can also block legitimate sign-in, administration, or business-application scripts. Inventory a script host in detection mode first and block it only for appropriate device groups. This does not replace AMSI or Threat Protection and is not blanket malware remediation.

Handle new applications automatically

Sophos can automatically include new applications in an already controlled category. This keeps policies current but expands their automatic impact. In a blocked category, a newly classified but operationally required product may therefore be blocked without separate approval.

Sophos marks New applications added to this category by Sophos as optional and warns against enabling it without careful consideration. Use it only when new catalogue entries in the category should deliberately be controlled automatically. The convenience of a current list does not replace change control; for blocked categories, periodic review followed by a pilot is usually easier to govern.

New GenAI category

Sophos now lists applications that use generative AI in the GenAI category. Depending on the platform, this includes desktop clients, local models, coding assistants and content tools. Existing programs such as Cursor, Microsoft Copilot, Ollama, Perplexity and Windsurf have been moved there from previous categories.

According to Sophos, reclassification does not change an application’s existing Allow or Block status. It does, however, change where the application is found in reports and policy maintenance. Re-inventory the GenAI category after a catalogue update. A blanket block is not a substitute for rules covering browser services, data classification and approved business AI applications.

Catalogue snapshot of August 18, 2026: Application Control 6.27

The 6.27 data update rolled out on August 18, 2026; the accompanying announcement appeared on August 19, 2026. This snapshot supplements the GenAI assessment above, but is neither a complete application list nor evidence for later releases. Examples relevant to policy maintenance include:

Windows verification: GitHub Copilot, Zed AI and Warp Terminal appear as GenAI in the announcement’s first catalogue list. That list has no platform heading of its own; these entries are therefore candidates for verification in the Windows pilot, not blanket evidence for every Windows version or application variant.
macOS: GitHub Copilot, Zed AI and Warp Terminal are also explicitly listed as GenAI in the separate macOS section. Verify the macOS classification independently of the first list; an entry on one platform does not imply identical detection on the other.

In addition, Notion Desktop App was renamed Notion AI and moved from BusinessIntelligenceTool to GenAI. During inventory, also search for the previous name and reconcile the existing allow or block decision with the new entry. Reclassification alone is no reason to replace an existing approval with a category block without checking it.

Publication happens in two stages: new entries may already be visible in the management interface 24 to 48 hours before the identity release. Only that release supplies the application’s detection data. For newly published entries, therefore wait for this window before assessing their Allow/Block effect. A visible entry or a saved setting does not yet prove effective control on the endpoint; nor does the window promise that every device will have updated by its end.

For this catalogue change, run the existing pilot separately on a Windows device and a macOS device, using the application version actually deployed:

Before the change, document the effective Application Control policy, the previous entry and its control state, and New applications added to this category by Sophos. If this category option is active and Block the detected application is enabled, newly added applications are blocked automatically. If that is not intended, disable the category option before rollout; doing so does not automatically allow entries that are already controlled.
After the publication window and a successful endpoint update, check the effective pilot policy under Policies. First scan the application in the existing detection mode, then look for the expected entry under Reports > Logs > Events using the Application Control filter. For Notion, reconcile the name Notion AI with the previous decision. Record the device name, operating system, application version and time as verification evidence.
Enable the intended block only in the pilot group, verify policy receipt and open the application again. Success means that the selected application is blocked, a matching event is present and a deliberately allowed comparison application still works. Do not assume that macOS shows the same desktop message as Windows.
If detection or blocking is missing, first check policy assignment, endpoint update, application version and the actual process. Do not instead block the GenAI category indiscriminately for all devices. To roll back, restore the affected application’s documented control state in the pilot policy, save it, wait for policy receipt and test startup again. Restore the category option to its previous value only if automatic handling of new entries is also wanted again.

Catalogue as of 6 October 2026: Application Control 6.28

The 6.28 data update rolled out on 6 October 2026; the final announcement dated 7 October 2026 confirms this. The advance announcement of 25 September described only the planned state. Use the final list for the inventory review, not the advance announcement:

The first list, without its own platform heading, includes, for example, ToDesk, Gorelo and TiFlux Agent as RemMan, and Google Antigravity IDE and Google Antigravity CLI as GenAI. Claude Science and Taskade Agent, both GenAI, were added there compared with the advance announcement. This list is not an explicitly labelled Windows compatibility matrix; check only programs and variants actually deployed.
The explicitly separate macOS section includes Claude Science, Taskade Agent and Google Antigravity IDE as GenAI, among others. These entries were already present there in the advance announcement. Additions to the first list are therefore not also new macOS additions; check detection and policy effect separately for each platform.

In addition, Google Antigravity moves from ProgrammingScriptTool to GenAI. Otter AI Assistant is now named Otter and moves from SystemTool to GenAI. Dynalist Obsidian becomes Obsidian, remaining in DocumentViewer. Search for both old and new names in reports and policy maintenance. The earlier statement about retaining control state when GenAI was introduced is not an explicit promise for these October changes: compare each affected entry’s actual Allow/Block state with the previous record.

For affected applications already present, the workflow above with detection, a platform-specific pilot and a limited rollback also applies to 6.28. Before a policy change, check category automation and Block the detected application in particular: if both are active, new entries may be blocked automatically. The 24 to 48 hours between the console entry and the identity release remain a publication window, not an update guarantee for every device. Inclusion in the catalogue is neither a malware verdict nor a recommendation to block all the applications mentioned.

If an application is missing

Not every product is immediately available in the Sophos catalogue. At the bottom of the Settings tab, Application Control Request opens the official request process. Until Sophos classifies the application, do not invent a category or signature to imitate catalogue detection.

⚠️ An unspecific Threat Protection exclusion is not a replacement for a missing Application Control entry. Application Control and malware exclusions solve different tasks.

Troubleshooting

If an expected application is not blocked, first check the effective policy, target group and policy order. Then check the application version, actual process and time of the last agent update. A catalogue entry does not mean that every variant or launcher is detected identically.

If a required application is blocked, correct the policy at application level and save it again. There is no need to disable Application Control globally. Then check on the affected device that the updated policy has arrived.

Build Sophos Fusion Endpoint policies correctly explains policy order and effective assignment. Introduce Sophos Endpoint Control policies in practice covers the overall rollout of control features.

Frequently asked questions

Should Application Control block immediately?

No. Detect applications and assess the Events first. A small pilot group then receives the first blocking policy.

Does Application Control replace malware protection?

No. Application Control enforces an operational software decision. Threat Protection continues to check for malware, exploits, ransomware and malicious behaviour.

Current application catalogue

Before changing a policy, use the current Sophos Controlled Applications catalogue to check whether the application is currently controllable and which category Sophos assigns to it. The vendor continually adds applications and new classifications to the catalogue.