diff --git a/deckhand/engine/layering.py b/deckhand/engine/layering.py
index 21abbcfd..67311721 100644
--- a/deckhand/engine/layering.py
+++ b/deckhand/engine/layering.py
@@ -265,7 +265,8 @@ class DocumentLayering(object):
                 details='The following pre-validation errors occurred '
                         '(schema, name, error): %s.' % val_errors)
 
-    def __init__(self, documents, substitution_sources=None, validate=True):
+    def __init__(self, documents, substitution_sources=None, validate=True,
+                 fail_on_missing_sub_src=True):
         """Contructor for ``DocumentLayering``.
 
         :param layering_policy: The document with schema
@@ -280,6 +281,9 @@ class DocumentLayering(object):
         :param validate: Whether to pre-validate documents using built-in
             schema validation. Default is True.
         :type validate: bool
+        :param fail_on_missing_sub_src: Whether to fail on a missing
+            substitution source. Default is True.
+        :type fail_on_missing_sub_src: bool
 
         :raises LayeringPolicyNotFound: If no LayeringPolicy was found among
             list of ``documents``.
@@ -349,7 +353,8 @@ class DocumentLayering(object):
         self._calc_all_document_children()
         self._substitution_sources = substitution_sources or []
         self.secrets_substitution = secrets_manager.SecretsSubstitution(
-            self._substitution_sources)
+            self._substitution_sources,
+            fail_on_missing_sub_src=fail_on_missing_sub_src)
 
         del self._documents_by_layer
         del self._documents_by_labels
diff --git a/deckhand/engine/secrets_manager.py b/deckhand/engine/secrets_manager.py
index 40bb5461..7e68248b 100644
--- a/deckhand/engine/secrets_manager.py
+++ b/deckhand/engine/secrets_manager.py
@@ -105,7 +105,8 @@ class SecretsManager(object):
 class SecretsSubstitution(object):
     """Class for document substitution logic for YAML files."""
 
-    def __init__(self, substitution_sources=None):
+    def __init__(self, substitution_sources=None,
+                 fail_on_missing_sub_src=True):
         """SecretSubstitution constructor.
 
         This class will automatically detect documents that require
@@ -115,9 +116,12 @@ class SecretsSubstitution(object):
         :param substitution_sources: List of documents that are potential
             sources for substitution. Should only include concrete documents.
         :type substitution_sources: List[dict]
+        :param bool fail_on_missing_sub_src: Whether to fail on a missing
+            substitution source. Default is True.
         """
 
         self._substitution_sources = {}
+        self._fail_on_missing_sub_src = fail_on_missing_sub_src
 
         for document in substitution_sources:
             if not isinstance(document, document_wrapper.DocumentDict):
@@ -175,11 +179,15 @@ class SecretsSubstitution(object):
                     message = ('Could not find substitution source document '
                               '[%s] %s among the provided '
                               '`substitution_sources`.', src_schema, src_name)
-                    LOG.error(message)
-                    raise errors.SubstitutionSourceNotFound(
-                        src_schema=src_schema, src_name=src_name,
-                        document_schema=document.schema,
-                        document_name=document.name)
+                    if self._fail_on_missing_sub_src:
+                        LOG.error(message)
+                        raise errors.SubstitutionSourceNotFound(
+                            src_schema=src_schema, src_name=src_name,
+                            document_schema=document.schema,
+                            document_name=document.name)
+                    else:
+                        LOG.warning(message)
+                        continue
 
                 # If the data is a dictionary, retrieve the nested secret
                 # via jsonpath_parse, else the secret is the primitive/string
diff --git a/deckhand/tests/unit/engine/test_document_layering.py b/deckhand/tests/unit/engine/test_document_layering.py
index b779ef5a..89090b3d 100644
--- a/deckhand/tests/unit/engine/test_document_layering.py
+++ b/deckhand/tests/unit/engine/test_document_layering.py
@@ -14,7 +14,10 @@
 
 import yaml
 
+import mock
+
 from deckhand.engine import layering
+from deckhand.engine import secrets_manager
 from deckhand import errors
 from deckhand import factories
 from deckhand.tests.unit import base as test_base
@@ -88,6 +91,34 @@ class TestDocumentLayering(test_base.DeckhandTestCase):
             self.assertEmpty(global_docs)
 
 
+class TestDocumentLayeringScenarios(TestDocumentLayering):
+
+    @mock.patch.object(secrets_manager, 'LOG', autospec=True)
+    def test_layering_with_missing_substitution_source_log_warning(self,
+                                                                   m_log):
+        """Validate that a missing substitution source document fails."""
+        mapping = {
+            "_SITE_SUBSTITUTIONS_1_": [{
+                "dest": {
+                    "path": ".c"
+                },
+                "src": {
+                    "schema": "example/Kind/v1",
+                    "name": "nowhere-to-be-found",
+                    "path": "."
+                }
+            }]
+        }
+        doc_factory = factories.DocumentFactory(2, [1, 1])
+        documents = doc_factory.gen_test(mapping, site_abstract=False)
+
+        self._test_layering(documents, site_expected={},
+                            fail_on_missing_sub_src=False)
+        self.assertTrue(m_log.warning.called)
+        self.assertRegex(m_log.warning.mock_calls[0][1][0][0],
+                         r'Could not find substitution source document .*')
+
+
 class TestDocumentLayering2Layers(TestDocumentLayering):
 
     def test_layering_default_scenario(self):