diff --git a/Apply-Template.ps1 b/Apply-Template.ps1
index 0d3f3d8e..d659670b 100644
--- a/Apply-Template.ps1
+++ b/Apply-Template.ps1
@@ -15,6 +15,20 @@ Param(
     [string]$Path
 )
 
+Push-Location $Path
+try {
+    # Look for our own initial commit in the target repo's history.
+    # If it's there, they've already switched to using git merge to freshen up.
+    # Using Apply-Template would just complicate future merges, so block it.
+    git log 05f49ce799c1f9cc696d53eea89699d80f59f833 ^HEAD | Out-Null
+    if ($LASTEXITCODE -eq 0) {
+        Write-Error 'The target repo already has Library.Template history merged into it. Use `git merge` instead of this script to freshen your repo. See the README.md file for details.'
+        exit 1
+    }
+} finally {
+    Pop-Location
+}
+
 Write-Host "Updating $Path"
 robocopy /mir $PSScriptRoot/azure-pipelines $Path/azure-pipelines
 robocopy /mir $PSScriptRoot/.devcontainer $Path/.devcontainer