diff --git a/doc/source/cli/cli.rst b/doc/source/cli/cli.rst
index 9e753930..0393af88 100644
--- a/doc/source/cli/cli.rst
+++ b/doc/source/cli/cli.rst
@@ -414,11 +414,24 @@ Please reference Shipyard's `CLI documentation`_ for information related to thes
 Specifies a UUID (8-4-4-4-12 format) that will be used to correlate logs,
 transactions, etc. in downstream activities triggered by this interaction.
 
+**-b / --buffer-mode** (Optional).  Default is auto.
+
+Set the buffer mode when uploading documents. Supported buffer modes
+include append, replace, auto.
+
+append: Add the collection to the Shipyard Buffer, only if that
+collection does not already exist in the Shipyard buffer.
+
+replace: Clear the Shipyard Buffer before adding the specified
+collection.
+
+auto: Let Pegleg determine the appropriate buffer mode to use.
+
 Usage:
 
 ::
 
-    ./pegleg.sh site <options> upload <site_name> --context-marker=<uuid>
+    ./pegleg.sh site <options> upload <site_name> --context-marker=<uuid> --buffer=<buffer>
 
 Site Secrets Group
 ------------------
diff --git a/pegleg/cli.py b/pegleg/cli.py
index 4fdd7661..28c61f8e 100644
--- a/pegleg/cli.py
+++ b/pegleg/cli.py
@@ -354,11 +354,25 @@ def lint_site(*, fail_on_missing_sub_src, exclude_lint, warn_lint, site_name):
          'interaction ',
     required=False,
     type=click.UUID)
+@click.option(
+    '-b',
+    '--buffer-mode',
+    'buffer_mode',
+    required=False,
+    default='auto',
+    show_default=True,
+    help='Set the buffer mode when uploading documents. Supported buffer '
+         'modes include append, replace, auto.\n'
+         'append: Add the collection to the Shipyard Buffer, only if that '
+         'collection does not already exist in the Shipyard buffer.\n'
+         'replace: Clear the Shipyard Buffer before adding the specified '
+         'collection.\n'
+         'auto: Let Pegleg determine the appropriate buffer mode to use.')
 @SITE_REPOSITORY_ARGUMENT
 @click.pass_context
 def upload(ctx, *, os_project_domain_name,
            os_user_domain_name, os_project_name, os_username,
-           os_password, os_auth_url, context_marker, site_name):
+           os_password, os_auth_url, context_marker, site_name, buffer_mode):
     if not ctx.obj:
         ctx.obj = {}
 
@@ -378,7 +392,7 @@ def upload(ctx, *, os_project_domain_name,
     ctx.obj['context_marker'] = str(context_marker)
     ctx.obj['site_name'] = site_name
 
-    click.echo(ShipyardHelper(ctx).upload_documents())
+    click.echo(ShipyardHelper(ctx, buffer_mode).upload_documents())
 
 
 @site.group(
diff --git a/pegleg/engine/exceptions.py b/pegleg/engine/exceptions.py
index f424858c..6be2622b 100644
--- a/pegleg/engine/exceptions.py
+++ b/pegleg/engine/exceptions.py
@@ -132,3 +132,13 @@ class SaltInsufficientLengthException(PeglegBaseException):
     """Exception raised when salt is too short."""
 
     message = 'PEGLEG_SALT must be at least 24 characters long.'
+
+
+#
+# Shipyard Helper Exceptions
+#
+
+class InvalidBufferModeException(PeglegBaseException):
+    """Exception raised when invalid buffer mode specified"""
+
+    message = 'BUFFER MODE must be one of: append, auto, replace'
diff --git a/pegleg/engine/util/shipyard_helper.py b/pegleg/engine/util/shipyard_helper.py
index 39f98b6f..f7537956 100644
--- a/pegleg/engine/util/shipyard_helper.py
+++ b/pegleg/engine/util/shipyard_helper.py
@@ -18,7 +18,7 @@ import uuid
 
 import yaml
 
-from pegleg.engine.exceptions import PeglegBaseException
+from pegleg.engine import exceptions
 from pegleg.engine.util import files
 from pegleg.engine.util.pegleg_secret_management import PeglegSecretManagement
 
@@ -29,14 +29,14 @@ from shipyard_client.api_client.shipyardclient_context import \
 LOG = logging.getLogger(__name__)
 
 
-class AuthValuesError(PeglegBaseException):
+class AuthValuesError(exceptions.PeglegBaseException):
     """Shipyard authentication failed. """
 
     def __init__(self, *, diagnostic):
         self.diagnostic = diagnostic
 
 
-class DocumentUploadError(PeglegBaseException):
+class DocumentUploadError(exceptions.PeglegBaseException):
     """Exception occurs while uploading documents"""
 
     def __init__(self, message):
@@ -52,7 +52,7 @@ class ShipyardHelper(object):
     4. Formats response from Shipyard api_client
     """
 
-    def __init__(self, context):
+    def __init__(self, context, buffer_mode='auto'):
         """
         Initializes params to be used by Shipyard
 
@@ -71,6 +71,7 @@ class ShipyardHelper(object):
         self.client_context = ShipyardClientContext(
             self.auth_vars, self.context_marker)
         self.api_client = ShipyardClient(self.client_context)
+        self.buffer_mode = buffer_mode
 
     def upload_documents(self):
         """Uploads documents to Shipyard """
@@ -82,10 +83,15 @@ class ShipyardHelper(object):
             # Append flag is not required for the first
             # collection being uploaded to Shipyard. It
             # is needed for subsequent collections.
-            if idx == 0:
-                buffer_mode = None
+            if self.buffer_mode == 'auto':
+                if idx == 0:
+                    buffer_mode = None
+                else:
+                    buffer_mode = 'append'
+            elif self.buffer_mode == 'append' or self.buffer_mode == 'replace':
+                buffer_mode = self.buffer_mode
             else:
-                buffer_mode = 'append'
+                raise exceptions.InvalidBufferModeException()
 
             # Decrypt the documents if encrypted
             pegleg_secret_mgmt = PeglegSecretManagement(