diff --git a/configure b/configure
index 48127ef87e..10c1117337 100755
--- a/configure
+++ b/configure
@@ -9033,15 +9033,26 @@ import pybind11
 #no need to check for python3, if you have python2, you don't have pybind11 (and vice-versa)
 "
     if echo "$testimport" | "$PYTHON_BIN" 1>/dev/null 2>/dev/null;  then
-       { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
-$as_echo "yes" >&6; }
+
        pyver=$($PYTHON_BIN -c "import sysconfig;print(sysconfig.get_config_var('VERSION'))")
        python_config=python${pyver}-config
-       PYBIND11_CFLAGS="$($PYTHON_BIN -m pybind11 --includes) -fvisibility=hidden"
-       PYTHON_CFLAGS=$(${python_config} --cflags --embed)
-       PYTHON_LDFLAGS=$(${python_config} --ldflags --embed)
-       #TODO: conda_fixup
-       PLUMED_CAN_PYCV=yes
+
+       if ${python_config} --ldflags --embed 1>/dev/null 2>/dev/null ;then
+          { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+          PYBIND11_CFLAGS="$($PYTHON_BIN -m pybind11 --includes) -fvisibility=hidden"
+          PYTHON_CFLAGS=$(${python_config} --cflags --embed)
+          PYTHON_LDFLAGS=$(${python_config} --ldflags --embed)
+          #TODO: conda_fixup
+          PLUMED_CAN_PYCV=yes
+        else
+          { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+          { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cannot enable pycv" >&5
+$as_echo "$as_me: WARNING: cannot enable pycv" >&2;}
+          { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \"PyCV needs python to be embeddable, please rebuild python\"" >&5
+$as_echo "$as_me: WARNING: \"PyCV needs python to be embeddable, please rebuild python\"" >&2;}
+       fi
     else
        { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
 $as_echo "no" >&6; }
diff --git a/configure.ac b/configure.ac
index 7c65c52008..76234fabee 100644
--- a/configure.ac
+++ b/configure.ac
@@ -859,14 +859,22 @@ import pybind11
 #no need to check for python3, if you have python2, you don't have pybind11 (and vice-versa)
 "
     if echo "$testimport" | "$PYTHON_BIN" 1>/dev/null 2>/dev/null;  then
-       AC_MSG_RESULT([yes])
+       
        pyver=$($PYTHON_BIN -c "import sysconfig;print(sysconfig.get_config_var('VERSION'))")
        python_config=python${pyver}-config
-       PYBIND11_CFLAGS="$($PYTHON_BIN -m pybind11 --includes) -fvisibility=hidden"
-       PYTHON_CFLAGS=$(${python_config} --cflags --embed)
-       PYTHON_LDFLAGS=$(${python_config} --ldflags --embed)
-       #TODO: conda_fixup
-       PLUMED_CAN_PYCV=yes
+       
+       if ${python_config} --ldflags --embed 1>/dev/null 2>/dev/null ;then
+          AC_MSG_RESULT([yes])
+          PYBIND11_CFLAGS="$($PYTHON_BIN -m pybind11 --includes) -fvisibility=hidden"
+          PYTHON_CFLAGS=$(${python_config} --cflags --embed)
+          PYTHON_LDFLAGS=$(${python_config} --ldflags --embed)
+          #TODO: conda_fixup
+          PLUMED_CAN_PYCV=yes
+        else
+          AC_MSG_RESULT([no])
+          AC_MSG_WARN([cannot enable pycv])
+          AC_MSG_WARN(["PyCV needs python to be embeddable, please rebuild python"])
+       fi
     else
        AC_MSG_RESULT([no])
        AC_MSG_WARN([cannot enable pycv])