diff --git a/CHANGELOG.md b/CHANGELOG.md
index e621e601b88e..183490b615e3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -129,6 +129,8 @@ v0.40.0 (2024-02-27)
 
 - Fix an issue where changing the configuration of `loki.write` would cause a panic. (@rfratto)
 
+- Fix issue where registry was not being properly deleted. (@mattdurham)
+
 ### Other changes
 
 - Removed support for Windows 2012 in line with Microsoft end of life. (@mattdurham)
diff --git a/packaging/grafana-agent-flow/windows/install_script.nsis b/packaging/grafana-agent-flow/windows/install_script.nsis
index 469a2cbd97b0..5e253890c2d5 100644
--- a/packaging/grafana-agent-flow/windows/install_script.nsis
+++ b/packaging/grafana-agent-flow/windows/install_script.nsis
@@ -193,6 +193,8 @@ Section "uninstall"
   RMDir /r "$APPDATA\${APPNAME}"     # Application data.
 
   # Remove service and uninstaller information from the registry.
-  DeleteRegKey HKLM "Software\Grafana\Grafana Agent Flow"
-  DeleteRegKey HKLM "Software\Microsoft\Windows\CurrentVersion\Uninstall\${APPNAME}"
+  nsExec::ExecToLog 'Reg.exe delete "HKLM\SOFTWARE\Grafana\Grafana Agent Flow"  /reg:64 /f'
+  Pop $0
+  nsExec::ExecToLog 'Reg.exe delete "HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\Uninstall\${APPNAME}"  /reg:64 /f'
+  Pop $0
 SectionEnd
diff --git a/packaging/grafana-agent/windows/install_script.nsis b/packaging/grafana-agent/windows/install_script.nsis
index b08a8216c691..a39ec0d4dc0d 100644
--- a/packaging/grafana-agent/windows/install_script.nsis
+++ b/packaging/grafana-agent/windows/install_script.nsis
@@ -229,6 +229,7 @@ Section "uninstall"
 
     RMDir /r $APPDATA\grafana-agent-wal
 
-    # Remove uninstaller information from the registry
-    DeleteRegKey HKLM "Software\Microsoft\Windows\CurrentVersion\Uninstall\${APPNAME}"
+    # Remove service and uninstaller information from the registry.
+    nsExec::ExecToLog 'Reg.exe delete "HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\Uninstall\${APPNAME}"  /reg:64 /f'
+    Pop $0
 SectionEnd