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Freedom251 › Blog › Malware Removal

How to Detect and Remove Malware on Your Minecraft Server

By Freedom251 Team · · 11 min read

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If a Minecraft plugin JAR looks malicious, treat the event as a server incident—not a routine plugin problem. Stop the Minecraft server, connected proxies, and related services; preserve a copy of the files and logs; scan every server and proxy offline; remove every flagged or untrusted JAR; rotate credentials; and rebuild the host when an attacker may have reached the operating system. Deleting one plugin and restarting is not enough to establish that the environment is clean.

What a compromised Minecraft server can look like

Malware on a Minecraft network may be hidden inside a plugin JAR, spread through more than one server, or leave changes outside the Minecraft directory. Symptoms can be subtle because a malicious plugin may continue providing its advertised feature while performing another task in the background.

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  • Unexpected plugin updates, unfamiliar JARs, or files obtained from unofficial mirrors.
  • Unexplained outbound connections, bandwidth use, CPU load, or memory consumption.
  • New operators, permission changes, accounts, scheduled tasks, or modified startup scripts.
  • Commands appearing in console or logs that no administrator recognizes.
  • Restarts, crashes, or configuration changes that begin shortly after a plugin installation or update.
  • Security software alerts naming a plugin, especially when the alert appeared after a signature update.

None of these signs alone proves malware. A generic antivirus detection can be a false positive, while a clean antivirus result does not prove that a server is safe. The reliable response combines containment, file provenance, hashes, scanner results, log timelines, and a decision about whether the host itself may have been accessed.

Contain the incident before investigating

Stop every process that can execute the suspected code

Stop the affected Minecraft process immediately. Also stop connected proxies, wrappers, scheduled restart services, control-panel agents, and any related service that can launch the server or load its plugins. Do not keep restarting the server to see whether a symptom disappears; every restart can execute the same code again and overwrite useful evidence.

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Keep all affected servers and proxies offline until the initial scan and evidence copy are complete. If several instances share a host, network storage, or plugin directory, treat them as part of the same incident rather than isolating only the instance where the first symptom appeared.

Preserve a forensic copy

Before deleting anything, copy the complete server directory to offline storage. Include plugin JARs, configuration files, startup scripts, the current log, rotated logs, crash reports, proxy files, and any system or authentication logs that can show access to the host. Preserve file timestamps and names where possible. Keep the copy read-only and separate from the machine being cleaned.

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At minimum, preserve:

  • Every .jar in each server and proxy plugin directory.
  • logs/latest.log, which PaperMC identifies as the newest server log.
  • Rotated logs, console output, crash reports, and panel audit records.
  • Operating-system authentication logs, scheduled-task data, firewall records, and service definitions.
  • Hashes or checksums for each file before removal.

Retain the scanner’s own output as evidence. MCAntiMalware documents a sequence of stopping the server, running java -jar MCAntiMalware.jar, and reviewing the generated AntiMalware/logs directory.

Inventory the entire network, not just the server showing symptoms

Make a written inventory before scanning. List every Minecraft server, proxy, host, container, plugin directory, and JAR. Record where each file came from, when it was installed or updated, and its checksum. Include offline or rarely used instances: an attacker may plant a copy where it will execute later.

Repeat the scan across every server and proxy in the network. The Spigot incident procedure specifically calls for scanning all servers and proxies, not only the machine where the alert first appeared. If a proxy forwards players to several backends, inspect both the proxy’s plugins and every backend’s plugins.

Build a file and provenance checklist

  • Does the JAR name match a plugin you intentionally installed?
  • Was it downloaded from the project’s official page or an established repository?
  • Does its version match the release you selected?
  • Does its checksum match a known-good copy from that release?
  • Was it copied to another server or proxy?
  • Did its installation coincide with a restart, new account, permission change, or outbound connection?

A JAR that cannot be tied to a deliberate installation should be treated as untrusted until proven otherwise. Do not keep it merely because the server appears to need it.

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Scan offline with Minecraft-aware tools

Use a dedicated plugin scanner

MCAntiMalware’s listing says it can scan directories and detect more than 1,000 malicious plugins. Its version 15.16 listing was updated September 4, 2025. Run it only after the server and proxies are stopped so the files cannot execute while you inspect them.

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  1. Stop every affected Minecraft server, proxy, and related launcher or restart service.
  2. Work from the preserved copy or a controlled clone when practical; keep the original evidence untouched.
  3. Run java -jar MCAntiMalware.jar from the directory containing the scanner.
  4. Review the generated AntiMalware/logs directory and record every detection, file path, and reason reported.
  5. Run the scan against each plugin and proxy directory in your inventory.
  6. Save the scanner output with your file hashes and incident timeline.

A plugin scanner is valuable for identifying suspicious JAR patterns and known malicious files, but it cannot certify the host operating system after an attacker has obtained host access. Treat a clean scan as one piece of evidence, not a complete clearance.

Correlate scanner findings with behavior

For each flagged file, compare the scanner result with:

  • Its origin and checksum.
  • Its install and update time.
  • Log entries immediately before and after installation.
  • New network destinations or unusual connection times.
  • Changes to operators, permissions, startup scripts, scheduled tasks, or user accounts.

PaperMC notes that malware can spread through compromised plugin-author accounts and may be difficult to detect. An apparently legitimate plugin name, publisher, or version number is therefore not sufficient proof of safety if the download source or checksum is wrong.

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Interpret antivirus alerts without overreacting—or ignoring them

Spigot warns that generic antivirus software can falsely report Java plugins as malware. Its platform notice says: “A recent Windows Defender signature change has caused very many plugins to be falsely reported as malware, usually as ‘Trojan:Script/Wacatac.B!ml’.” A single Defender or other endpoint alert is a lead, not a verdict.

Raise confidence when at least one independent signal agrees:

  • A Minecraft-specific scanner flags the same JAR.
  • The checksum differs from the official release.
  • Decompilation or code review reveals unexpected loading, command execution, credential collection, or network behavior.
  • The file came from an unofficial mirror or a publisher account known to have been compromised.
  • Logs or network monitoring show activity that the plugin’s documented purpose does not require.

Lower confidence in an alert only when you can reproduce the result against a verified official JAR, compare its checksum, and find no suspicious behavior. Do not create an antivirus exclusion simply to get the server running again.

Remove malicious or untrusted plugins safely

Delete every affected copy

With the server and proxies still offline, remove every flagged JAR and every copy that cannot be trusted. Search all plugin directories, backup staging areas, proxy directories, containers, and alternate server instances. Removing only the copy named in an alert leaves an easy route for reinfection.

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Keep the original files in the preserved evidence copy. Delete or quarantine the executable copies from the environment that will be restored. Do not execute a JAR to test whether it is safe.

Download replacements from trusted project pages

Obtain clean replacements from the plugin’s official project page or an established repository. PaperMC identifies Hangar, Modrinth, and BukkitDev as plugin sources and directs administrators toward official plugin sources. Verify the project name, version, publisher, release notes, and checksum before copying a replacement into a server.

Do not restore executable JARs or startup scripts from an unknown backup. A backup is useful only if you know when it was created, where it came from, and that it predates the compromise or has been inspected.

Rescan before the first restart

  1. Place only the verified replacement JARs in a clean staging directory.
  2. Run the scanner against that complete set, including proxy plugins.
  3. Compare the resulting file list with your inventory and confirm that no unexpected JAR remains.
  4. Check configuration and startup scripts for added commands, remote downloads, or altered paths.
  5. Start the server only after the clean set and its evidence record are complete.

Assume credentials are exposed when the host may have been reached

A malicious plugin can expose secrets available to the Minecraft process. If the attacker may have obtained operating-system access, the risk is broader: panel credentials, SSH or FTP accounts, database passwords, RCON secrets, bot tokens, and credentials stored in scripts or environment files may all be compromised.

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From a separate, trusted machine:

  • Rotate panel, SSH, FTP, database, RCON, Discord-bot, and Minecraft credentials.
  • Invalidate API keys, session tokens, deploy keys, and bot tokens rather than merely changing their labels.
  • Review newly created users, operators, permissions, SSH keys, scheduled tasks, and service accounts.
  • Revoke access for people or integrations that no longer need it.
  • Change shared passwords anywhere else they were reused.

Do not rotate secrets from the potentially compromised host; a keylogger or malicious process could capture the replacements.

When to rebuild the operating system

Deleting a malicious plugin is not enough if an attacker had host access. The Spigot incident guidance recommends backing up data and reinstalling the operating system after removing malicious JARs because the original plugin may have created persistence elsewhere.

Rebuild from trusted installation media when you cannot establish that the compromise was confined to a JAR, or when you find altered system services, users, scheduled tasks, startup scripts, SSH keys, or other host-level changes. A rebuild should include:

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  1. Preserving evidence and vetted data before wiping the host.
  2. Installing the operating system from trusted media.
  3. Applying current security patches before exposing the machine to players.
  4. Installing the server software and required runtime from trusted sources.
  5. Restoring only inspected worlds, configuration, and non-executable data.
  6. Installing verified plugins and scanning the final set before launch.
  7. Recreating least-privilege accounts and rotating credentials again if they were present during the compromise.

If you choose not to rebuild, document why the evidence supports a plugin-only compromise and apply equivalent host checks. Uncertainty about persistence is itself a reason to rebuild.

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Restore backups without restoring the infection

PaperMC’s troubleshooting guidance begins with “Stop Your Server And Take A Backup.” A functioning, separate backup is essential, but not every backup is safe to restore. Preserve a known-good copy of worlds and configuration while the incident is investigated, then inspect the backup before use.

  • Identify the backup’s creation time and storage location.
  • Check whether the backup contains plugin JARs, startup scripts, or other executable content.
  • Scan and review those files before restoring them.
  • Prefer restoring world data and vetted configuration separately from executable components.
  • Keep an untouched copy in case later evidence changes your assessment.

Never let a convenient restore overwrite the evidence copy or reintroduce an untrusted plugin.

Start the recovered server cautiously

After the clean rebuild or verified plugin replacement, start one server at a time. Use least-privilege service accounts, restrict administrative access, and keep proxies and backends separated until each has passed its checks.

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Watch logs/latest.log and rotated logs closely after startup and after every plugin update. PaperMC recommends watching server logs after updates. Also monitor outbound connections, resource use, account changes, operator assignments, permission changes, and unexpected restarts. A clean first launch is not proof that persistence is absent; continued observation is part of recovery.

Choose the right level of response

Response or evidence What it contributes Important limitation When to use it
Offline Minecraft-plugin scan Finds suspicious JAR patterns and known malicious plugins; MCAntiMalware supports directory scanning. Cannot prove the host operating system is clean after host access. Every suspected incident, before removal and before restart.
Generic endpoint antivirus Provides an additional malware signal for the host and files. Java plugins can be falsely flagged, including the Wacatac.B!ml alert described by Spigot. Use as a complementary control and corroborate the result.
Logs, hashes, and provenance review Creates a reproducible timeline and helps distinguish an official release from a modified copy. Evidence collection does not remove persistence. Always, especially when deciding whether a detection is a false positive.
Credential rotation Limits damage from exposed passwords, tokens, keys, and service secrets. Does not remove malicious files or host-level persistence. Whenever the plugin or host could read credentials.
Operating-system rebuild Removes unknown host-level changes and provides a trusted base for reinstallation. Requires downtime and careful data restoration. When host access or persistence cannot be ruled out.

NIST describes antivirus, spyware-removal tools, intrusion prevention, and firewalls as complementary controls with limitations. A Minecraft-specific scanner and general endpoint controls serve different purposes; neither replaces incident response.

Threats that look like ordinary server problems

Microsoft has documented MCCrash, a botnet targeting private Minecraft servers with server and Minecraft commands, and described Defender detections for the malware involved. That context matters when a server suddenly shows unusual resource use, command activity, or network behavior. Treat those changes as potentially hostile until logs, file provenance, and host evidence explain them.

A performance spike may be a bug or a botnet workload. A new command may be an administrator or an attacker. The distinction comes from correlating timestamps, accounts, plugin changes, network connections, and checksums—not from the symptom alone.

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Common recovery mistakes and how to avoid them

Restarting before copying logs

Repeated restarts can overwrite the event sequence and execute the suspected JAR again. Stop first, preserve logs/latest.log and rotated logs, then scan.

Scanning only the server named in the alert

Compromised files may exist on another backend, proxy, container, or staging directory. Build an inventory and repeat the scan everywhere.

Trusting a familiar plugin name

An attacker can use a legitimate project name, a modified release, or a compromised publisher account. Verify the source, version, checksum, and behavior.

Deleting the JAR and keeping the same credentials

If the plugin could read secrets, assume those secrets were exposed. Rotate them from a clean machine and invalidate tokens.

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Restoring a complete old backup

An old backup may contain the same malicious JAR or altered startup script. Restore inspected data and reinstall executable components from trusted sources.

Calling the host clean after one scanner reports no findings

A plugin scanner can miss persistence outside the Minecraft directories. If host access is plausible, rebuild the operating system or perform a documented host-level investigation before declaring recovery complete.

Post-recovery checklist

  • All servers, proxies, and launch services were stopped during preservation and scanning.
  • A separate evidence copy contains the original JARs, configurations, logs, and relevant host records.
  • Every server and proxy directory was inventoried and scanned.
  • Flagged and untrusted JARs were removed from every copy.
  • Replacement plugins came from official project pages or established repositories and were rescanned.
  • Panel, SSH/FTP, database, RCON, bot, and Minecraft credentials were rotated from a clean machine.
  • Tokens, keys, new accounts, operators, permissions, and scheduled tasks were reviewed.
  • Only inspected data was restored; unknown executable files were excluded.
  • The operating system was rebuilt when host access or persistence could not be ruled out.
  • Logs, outbound traffic, resource use, and account changes are being watched after recovery and updates.

Bottom line

A suspicious Minecraft plugin is an incident until evidence shows otherwise. Contain first, preserve evidence, scan every server and proxy offline, verify provenance and hashes, remove every untrusted JAR, rotate exposed credentials, and rebuild the host when persistence is possible. Keep separate backups and continue monitoring after the first clean startup; recovery is complete only when both the executable files and the environment that ran them are trustworthy.

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