diff --git a/scripts/package-count.sh b/scripts/package-count.sh
index 8d5b2ab0e8..4d2b845ec6 100644
--- a/scripts/package-count.sh
+++ b/scripts/package-count.sh
@@ -18,7 +18,16 @@ infer_package_manager() {
   elif [[ -f "vlt-lock.json" ]]; then
     echo "vlt"
   elif [[ -f "pnpm-lock.yaml" ]]; then
-    echo "pnpm"
+    # pnpm (v11, TypeScript) and pacquet (pnpm v12, Rust) both leave a
+    # pnpm-lock.yaml, so the lockfile alone can't tell them apart. The
+    # installer records its own version in node_modules/.modules.yaml
+    # (packageManager: pnpm@<version>); v12+ is pacquet.
+    pnpm_major=$(sed -n "s/^packageManager: ['\"]\{0,1\}pnpm@\([0-9][0-9]*\).*/\1/p" node_modules/.modules.yaml 2>/dev/null | head -1)
+    if [[ -n "$pnpm_major" && "$pnpm_major" -ge 12 ]]; then
+      echo "pacquet"
+    else
+      echo "pnpm"
+    fi
   elif [[ -f "yarn.lock" ]]; then
     if [[ -f ".yarnrc.yml" ]] && command -v yarn >/dev/null 2>&1; then
       yarn_version=$(yarn -v 2>/dev/null || echo "")
diff --git a/scripts/variations/lockfile+node_modules.sh b/scripts/variations/lockfile+node_modules.sh
index df22d610d1..c86c72cf07 100644
--- a/scripts/variations/lockfile+node_modules.sh
+++ b/scripts/variations/lockfile+node_modules.sh
@@ -4,8 +4,11 @@ set -Eeuxo pipefail
 # Load common variables
 source "$1/variations/common.sh"
 
-# Prepare command base for each run
-BENCH_PREPARE_BASE="sleep 1; bash $BENCH_SCRIPTS/clean-helpers.sh clean_all_cache clean_package_manager_files"
+# Prepare command base for each run.
+# clean_package_manager_field must run AFTER clean_all_cache: the corepack
+# yarn cache cleans re-pin devEngines.packageManager (yarn) into package.json,
+# which makes npm and pnpm refuse to run entirely (see clean_all).
+BENCH_PREPARE_BASE="sleep 1; bash $BENCH_SCRIPTS/clean-helpers.sh clean_all_cache clean_package_manager_files clean_package_manager_field"
 
 # Run the benchmark suite
 # When running a cache benchmark, we want to clean up only the node_modules
diff --git a/scripts/variations/lockfile.sh b/scripts/variations/lockfile.sh
index 6ac11e925a..c06d61a104 100644
--- a/scripts/variations/lockfile.sh
+++ b/scripts/variations/lockfile.sh
@@ -4,8 +4,11 @@ set -Eeuxo pipefail
 # Load common variables
 source "$1/variations/common.sh"
 
-# Prepare command base for each run
-BENCH_PREPARE_BASE="sleep 1; bash $BENCH_SCRIPTS/clean-helpers.sh clean_all_cache clean_node_modules clean_package_manager_files"
+# Prepare command base for each run.
+# clean_package_manager_field must run AFTER clean_all_cache: the corepack
+# yarn cache cleans re-pin devEngines.packageManager (yarn) into package.json,
+# which makes npm and pnpm refuse to run entirely (see clean_all).
+BENCH_PREPARE_BASE="sleep 1; bash $BENCH_SCRIPTS/clean-helpers.sh clean_all_cache clean_node_modules clean_package_manager_files clean_package_manager_field"
 
 # Run the benchmark suite
 # When running a cache benchmark, we want to clean up only the node_modules
diff --git a/scripts/variations/node_modules.sh b/scripts/variations/node_modules.sh
index 3264eeba70..8cedd44859 100644
--- a/scripts/variations/node_modules.sh
+++ b/scripts/variations/node_modules.sh
@@ -4,8 +4,11 @@ set -Eeuxo pipefail
 # Load common variables
 source "$1/variations/common.sh"
 
-# Prepare command base for each run
-BENCH_PREPARE_BASE="sleep 1; bash $BENCH_SCRIPTS/clean-helpers.sh clean_all_cache clean_lockfiles clean_package_manager_files"
+# Prepare command base for each run.
+# clean_package_manager_field must run AFTER clean_all_cache: the corepack
+# yarn cache cleans re-pin devEngines.packageManager (yarn) into package.json,
+# which makes npm and pnpm refuse to run entirely (see clean_all).
+BENCH_PREPARE_BASE="sleep 1; bash $BENCH_SCRIPTS/clean-helpers.sh clean_all_cache clean_lockfiles clean_package_manager_files clean_package_manager_field"
 
 # Run the benchmark suite
 # When running a cache benchmark, we want to clean up only the node_modules