diff --git a/scripts/bootstrap.sh b/scripts/bootstrap.sh
index aecf8bb..68f26c4 100644
--- a/scripts/bootstrap.sh
+++ b/scripts/bootstrap.sh
@@ -316,6 +316,15 @@ PY
 
       if "$VENV_PY" -c 'import importlib; importlib.import_module("CLI")' >/dev/null 2>&1; then
         echo "OK: top-level 'CLI' is now importable (after .pth)." >&2
+
+        # Also verify we can run the packaged entrypoint using module form. If this fails
+        # it suggests site-packages/.pth wasn't processed reliably by the interpreter.
+        if "$VENV_PY" -m medeia_macina.cli_entry --help >/dev/null 2>&1; then
+          echo "OK: 'python -m medeia_macina.cli_entry' runs in the venv." >&2
+        else
+          echo "ERROR: 'python -m medeia_macina.cli_entry' failed in the venv despite .pth being written; aborting." >&2
+          exit 6
+        fi
       else
         echo "ERROR: top-level 'CLI' still not importable after writing .pth ($pth_file)." >&2
         exit 6
@@ -528,12 +537,7 @@ PY
   echo "MM_DEBUG: end diagnostics" >&2
 fi
 
-# Packaged console script in the venv if available
-if [ -x "$VENV/bin/mm" ]; then
-  exec "$VENV/bin/mm" "$@"
-fi
-
-# Prefer venv's python3, then venv's python
+# Prefer venv's python3, then venv's python (module invocation - more deterministic)
 if [ -x "$VENV/bin/python3" ]; then
   exec "$VENV/bin/python3" -m medeia_macina.cli_entry "$@"
 fi
@@ -541,6 +545,11 @@ if [ -x "$VENV/bin/python" ]; then
   exec "$VENV/bin/python" -m medeia_macina.cli_entry "$@"
 fi
 
+# Fallback: packaged console script in the venv (older pip-generated wrapper)
+if [ -x "$VENV/bin/mm" ]; then
+  exec "$VENV/bin/mm" "$@"
+fi
+
 # Fallback to system python3, then system python (only if it's Python 3)
 if command -v python3 >/dev/null 2>&1; then
   exec python3 -m medeia_macina.cli_entry "$@"
diff --git a/scripts/setup.py b/scripts/setup.py
index 2d09b23..a698eac 100644
--- a/scripts/setup.py
+++ b/scripts/setup.py
@@ -304,11 +304,10 @@ SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 REPO="$SCRIPT_DIR"
 VENV="$REPO/.venv"
 PY="$VENV/bin/python"
-CLI_SCRIPT="$REPO/CLI.py"
 if [ -x "$PY" ]; then
-  exec "$PY" "$CLI_SCRIPT" "$@"
+  exec "$PY" -m medeia_macina.cli_entry "$@"
 else
-  exec python "$CLI_SCRIPT" "$@"
+  exec python -m medeia_macina.cli_entry "$@"
 fi
 """
             try:
@@ -323,10 +322,10 @@ $repo = $scriptDir
 $venv = Join-Path $repo '.venv'
 $py = Join-Path $venv 'Scripts\python.exe'
 $cli = Join-Path $repo 'CLI.py'
-if (Test-Path $py) { & $py $cli @args; exit $LASTEXITCODE }
-if (Test-Path $cli) { & $py $cli @args; exit $LASTEXITCODE }
+if (Test-Path $py) { & $py -m medeia_macina.cli_entry @args; exit $LASTEXITCODE }
+if (Test-Path $cli) { & python $cli @args; exit $LASTEXITCODE }
 # fallback
-python $cli @args
+python -m medeia_macina.cli_entry @args
 """
             try:
                 ps1.write_text(ps1_text, encoding="utf-8")
@@ -336,9 +335,10 @@ python $cli @args
             bat_text = (
                 "@echo off\r\n"
                 "set SCRIPT_DIR=%~dp0\r\n"
-                "if exist \"%SCRIPT_DIR%\\.venv\\Scripts\\python.exe\" \"%SCRIPT_DIR%\\.venv\\Scripts\\python.exe\" \"%SCRIPT_DIR%\\CLI.py\" %*\r\n"
+                "if exist \"%SCRIPT_DIR%\\.venv\\Scripts\\python.exe\" \"%SCRIPT_DIR%\\.venv\\Scripts\\python.exe\" -m medeia_macina.cli_entry %*\r\n"
                 "if exist \"%SCRIPT_DIR%\\CLI.py\" python \"%SCRIPT_DIR%\\CLI.py\" %*\r\n"
                 "python -m medeia_macina.cli_entry %*\r\n"
+                "python -m medeia_macina.cli_entry %*\r\n"
             )
             try:
                 bat.write_text(bat_text, encoding="utf-8")