diff --git a/lib/iris/config.py b/lib/iris/config.py
index e14ac058a4..2bb82924a2 100644
--- a/lib/iris/config.py
+++ b/lib/iris/config.py
@@ -1,4 +1,4 @@
-# (C) British Crown Copyright 2010 - 2016, Met Office
+# (C) British Crown Copyright 2010 - 2017, Met Office
 #
 # This file is part of Iris.
 #
@@ -66,8 +66,10 @@
 
 from __future__ import (absolute_import, division, print_function)
 from six.moves import (filter, input, map, range, zip)  # noqa
-
+import six
 from six.moves import configparser
+
+import contextlib
 import os.path
 import warnings
 
@@ -154,3 +156,106 @@ def get_dir_option(section, option, default=None):
 
 
 IMPORT_LOGGER = get_option(_LOGGING_SECTION, 'import_logger')
+
+
+#################
+# Runtime options
+
+class NetCDF(object):
+    """Control Iris NetCDF options."""
+
+    def __init__(self, conventions_override=None):
+        """
+        Set up NetCDF processing options for Iris.
+
+        Currently accepted kwargs:
+
+        * conventions_override (bool):
+            Define whether the CF Conventions version (e.g. `CF-1.6`) set when
+            saving a cube to a NetCDF file should be defined by
+            Iris (the default) or the cube being saved.
+
+            If `False` (the default), specifies that Iris should set the
+            CF Conventions version when saving cubes as NetCDF files.
+            If `True`, specifies that the cubes being saved to NetCDF should
+            set the CF Conventions version for the saved NetCDF files.
+
+        Example usages:
+
+        * Specify, for the lifetime of the session, that we want all cubes
+          written to NetCDF to define their own CF Conventions versions::
+
+            iris.config.netcdf.conventions_override = True
+            iris.save('my_cube', 'my_dataset.nc')
+            iris.save('my_second_cube', 'my_second_dataset.nc')
+
+        * Specify, with a context manager, that we want a cube written to
+          NetCDF to define its own CF Conventions version::
+
+            with iris.config.netcdf.context(conventions_override=True):
+                iris.save('my_cube', 'my_dataset.nc')
+
+        """
+        # Define allowed `__dict__` keys first.
+        self.__dict__['conventions_override'] = None
+
+        # Now set specific values.
+        setattr(self, 'conventions_override', conventions_override)
+
+    def __repr__(self):
+        msg = 'NetCDF options: {}.'
+        # Automatically populate with all currently accepted kwargs.
+        options = ['{}={}'.format(k, v)
+                   for k, v in six.iteritems(self.__dict__)]
+        joined = ', '.join(options)
+        return msg.format(joined)
+
+    def __setattr__(self, name, value):
+        if name not in self.__dict__:
+            # Can't add new names.
+            msg = 'Cannot set option {!r} for {} configuration.'
+            raise AttributeError(msg.format(name, self.__class__.__name__))
+        if value is None:
+            # Set an unset value to the name's default.
+            value = self._defaults_dict[name]['default']
+        if self._defaults_dict[name]['options'] is not None:
+            # Replace a bad value with a good one if there is a defined set of
+            # specified good values. If there isn't, we can assume that
+            # anything goes.
+            if value not in self._defaults_dict[name]['options']:
+                good_value = self._defaults_dict[name]['default']
+                wmsg = ('Attempting to set invalid value {!r} for '
+                        'attribute {!r}. Defaulting to {!r}.')
+                warnings.warn(wmsg.format(value, name, good_value))
+                value = good_value
+        self.__dict__[name] = value
+
+    @property
+    def _defaults_dict(self):
+        # Set this as a property so that it isn't added to `self.__dict__`.
+        return {'conventions_override': {'default': False,
+                                         'options': [True, False]},
+                }
+
+    @contextlib.contextmanager
+    def context(self, **kwargs):
+        """
+        Allow temporary modification of the options via a context manager.
+        Accepted kwargs are the same as can be supplied to the Option.
+
+        """
+        # Snapshot the starting state for restoration at the end of the
+        # contextmanager block.
+        starting_state = self.__dict__.copy()
+        # Update the state to reflect the requested changes.
+        for name, value in six.iteritems(kwargs):
+            setattr(self, name, value)
+        try:
+            yield
+        finally:
+            # Return the state to the starting state.
+            self.__dict__.clear()
+            self.__dict__.update(starting_state)
+
+
+netcdf = NetCDF()
diff --git a/lib/iris/fileformats/netcdf.py b/lib/iris/fileformats/netcdf.py
index 527ebfabb5..11565299fb 100644
--- a/lib/iris/fileformats/netcdf.py
+++ b/lib/iris/fileformats/netcdf.py
@@ -1,4 +1,4 @@
-# (C) British Crown Copyright 2010 - 2016, Met Office
+# (C) British Crown Copyright 2010 - 2017, Met Office
 #
 # This file is part of Iris.
 #
@@ -2244,7 +2244,12 @@ def is_valid_packspec(p):
                        shuffle, fletcher32, contiguous, chunksizes, endian,
                        least_significant_digit, packing=packspec)
 
-        conventions = CF_CONVENTIONS_VERSION
+        if iris.config.netcdf.conventions_override:
+            # Set to the default if custom conventions are not available.
+            conventions = cube.attributes.get('Conventions',
+                                              CF_CONVENTIONS_VERSION)
+        else:
+            conventions = CF_CONVENTIONS_VERSION
 
         # Perform a CF patch of the conventions attribute.
         cf_profile_available = (iris.site_configuration.get('cf_profile') not
diff --git a/lib/iris/tests/unit/config/__init__.py b/lib/iris/tests/unit/config/__init__.py
new file mode 100644
index 0000000000..dd625e1e91
--- /dev/null
+++ b/lib/iris/tests/unit/config/__init__.py
@@ -0,0 +1,20 @@
+# (C) British Crown Copyright 2017, Met Office
+#
+# This file is part of Iris.
+#
+# Iris is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# Iris is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with Iris.  If not, see <http://www.gnu.org/licenses/>.
+"""Unit tests for the :mod:`iris.config` module."""
+
+from __future__ import (absolute_import, division, print_function)
+from six.moves import (filter, input, map, range, zip)  # noqa
diff --git a/lib/iris/tests/unit/config/test_NetCDF.py b/lib/iris/tests/unit/config/test_NetCDF.py
new file mode 100644
index 0000000000..3929319854
--- /dev/null
+++ b/lib/iris/tests/unit/config/test_NetCDF.py
@@ -0,0 +1,60 @@
+# (C) British Crown Copyright 2017, Met Office
+#
+# This file is part of Iris.
+#
+# Iris is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# Iris is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with Iris.  If not, see <http://www.gnu.org/licenses/>.
+"""Unit tests for the `iris.config.NetCDF` class."""
+
+from __future__ import (absolute_import, division, print_function)
+from six.moves import (filter, input, map, range, zip)  # noqa
+import six
+
+# Import iris.tests first so that some things can be initialised before
+# importing anything else.
+import iris.tests as tests
+
+import warnings
+
+import iris.config
+
+
+class Test(tests.IrisTest):
+    def setUp(self):
+        self.options = iris.config.NetCDF()
+
+    def test_basic(self):
+        self.assertFalse(self.options.conventions_override)
+
+    def test_enabled(self):
+        self.options.conventions_override = True
+        self.assertTrue(self.options.conventions_override)
+
+    def test_bad_value(self):
+        # A bad value should be ignored and replaced with the default value.
+        bad_value = 'wibble'
+        with warnings.catch_warnings(record=True) as w:
+            warnings.simplefilter('always')
+            self.options.conventions_override = bad_value
+        self.assertFalse(self.options.conventions_override)
+        exp_wmsg = 'Attempting to set invalid value {!r}'.format(bad_value)
+        six.assertRegex(self, str(w[0].message), exp_wmsg)
+
+    def test__contextmgr(self):
+        with self.options.context(conventions_override=True):
+            self.assertTrue(self.options.conventions_override)
+        self.assertFalse(self.options.conventions_override)
+
+
+if __name__ == '__main__':
+    tests.main()
diff --git a/lib/iris/tests/unit/fileformats/netcdf/test_save.py b/lib/iris/tests/unit/fileformats/netcdf/test_save.py
index b1b76f56ce..936de128a6 100644
--- a/lib/iris/tests/unit/fileformats/netcdf/test_save.py
+++ b/lib/iris/tests/unit/fileformats/netcdf/test_save.py
@@ -1,4 +1,4 @@
-# (C) British Crown Copyright 2014 - 2016, Met Office
+# (C) British Crown Copyright 2014 - 2017, Met Office
 #
 # This file is part of Iris.
 #
@@ -23,6 +23,7 @@
 # importing anything else.
 import iris.tests as tests
 
+import mock
 import netCDF4 as nc
 import numpy as np
 
@@ -32,20 +33,48 @@
 from iris.tests.stock import lat_lon_cube
 
 
-class Test_attributes(tests.IrisTest):
-    def test_custom_conventions(self):
+class Test_conventions(tests.IrisTest):
+    def setUp(self):
+        self.cube = Cube([0])
+        self.custom_conventions = 'convention1 convention2'
+        self.cube.attributes['Conventions'] = self.custom_conventions
+        self.options = iris.config.netcdf
+
+    def test_custom_conventions__ignored(self):
         # Ensure that we drop existing conventions attributes and replace with
         # CF convention.
-        cube = Cube([0])
-        cube.attributes['Conventions'] = 'convention1 convention2'
-
         with self.temp_filename('.nc') as nc_path:
-            save(cube, nc_path, 'NETCDF4')
+            save(self.cube, nc_path, 'NETCDF4')
             ds = nc.Dataset(nc_path)
             res = ds.getncattr('Conventions')
             ds.close()
         self.assertEqual(res, CF_CONVENTIONS_VERSION)
 
+    def test_custom_conventions__allowed(self):
+        # Ensure that existing conventions attributes are passed through if the
+        # relevant Iris option is set.
+        with mock.patch.object(self.options, 'conventions_override', True):
+            with self.temp_filename('.nc') as nc_path:
+                save(self.cube, nc_path, 'NETCDF4')
+                ds = nc.Dataset(nc_path)
+                res = ds.getncattr('Conventions')
+                ds.close()
+        self.assertEqual(res, self.custom_conventions)
+
+    def test_custom_conventions__allowed__missing(self):
+        # Ensure the default conventions attribute is set if the relevant Iris
+        # option is set but there is no custom conventions attribute.
+        del self.cube.attributes['Conventions']
+        with mock.patch.object(self.options, 'conventions_override', True):
+            with self.temp_filename('.nc') as nc_path:
+                save(self.cube, nc_path, 'NETCDF4')
+                ds = nc.Dataset(nc_path)
+                res = ds.getncattr('Conventions')
+                ds.close()
+        self.assertEqual(res, CF_CONVENTIONS_VERSION)
+
+
+class Test_attributes(tests.IrisTest):
     def test_attributes_arrays(self):
         # Ensure that attributes containing NumPy arrays can be equality
         # checked and their cubes saved as appropriate.