diff --git a/eng/build.ps1 b/eng/build.ps1
index 4bfe9bad1825d5..9aead19dcdd9ff 100644
--- a/eng/build.ps1
+++ b/eng/build.ps1
@@ -395,6 +395,9 @@ if ($bootstrap -eq $True) {
   $config = $((Get-Culture).TextInfo.ToTitleCase($configuration[0]))
   $bootstrapArguments += " -configuration $config"
 
+  # Set a different path for prebuilt usage tracking for the bootstrap build.
+  $bootstrapArguments += " /p:TrackPrebuiltUsageReportFile=$PSScriptRoot/../artifacts/log/bootstrap-prebuilt-usage.xml"
+
   $bootstrapArguments += " /p:Subset=bootstrap /bl:$PSScriptRoot/../artifacts/log/$config/bootstrap.binlog"
   Invoke-Expression "& `"$PSScriptRoot/common/build.ps1`" $bootstrapArguments"
 
diff --git a/eng/build.sh b/eng/build.sh
index 43ed2988fa17d5..3720bdb52f8e9e 100755
--- a/eng/build.sh
+++ b/eng/build.sh
@@ -608,7 +608,9 @@ if [[ "$bootstrap" == "1" ]]; then
       bootstrapArguments+=("$argument")
     fi
   done
-  "$scriptroot/common/build.sh" ${bootstrapArguments[@]+"${bootstrapArguments[@]}"} /p:Subset=bootstrap -bl:$scriptroot/../artifacts/log/$bootstrapConfig/bootstrap.binlog
+
+  # Set a different path for prebuilt usage tracking for the bootstrap build.
+  "$scriptroot/common/build.sh" ${bootstrapArguments[@]+"${bootstrapArguments[@]}"} /p:Subset=bootstrap /p:TrackPrebuiltUsageReportFile=$scriptroot/../artifacts/log/bootstrap-prebuilt-usage.xml -bl:$scriptroot/../artifacts/log/$bootstrapConfig/bootstrap.binlog
 
   # Remove artifacts from the bootstrap build so the product build is a "clean" build.
   echo "Cleaning up artifacts from bootstrap build..."