diff --git a/features/plugin-activate.feature b/features/plugin-activate.feature
index a2c32c2a..ed334553 100644
--- a/features/plugin-activate.feature
+++ b/features/plugin-activate.feature
@@ -115,3 +115,13 @@ Feature: Activate WordPress plugins
       Success: Activated 1 of 1 plugins.
       """
     And the return code should be 0
+
+  Scenario: Excluding a missing plugin should not throw an error
+    Given a WP install
+    And I run `wp plugin activate --all --exclude=missing-plugin`
+    Then STDERR should be empty
+    And STDOUT should contain:
+      """
+      Success:
+      """
+    And the return code should be 0
diff --git a/features/plugin-deactivate.feature b/features/plugin-deactivate.feature
index 5cbd8e0d..7a679110 100644
--- a/features/plugin-deactivate.feature
+++ b/features/plugin-deactivate.feature
@@ -94,3 +94,13 @@ Feature: Deactivate WordPress plugins
       Error: Please specify one or more plugins, or use --all.
       """
     And STDOUT should be empty
+
+  Scenario: Excluding a missing plugin should not throw an error
+    Given a WP install
+    And I run `wp plugin deactivate --all --exclude=missing-plugin`
+    Then STDERR should be empty
+    And STDOUT should contain:
+      """
+      Success:
+      """
+    And the return code should be 0
diff --git a/features/plugin-delete.feature b/features/plugin-delete.feature
index 3ec4c472..a0cdb822 100644
--- a/features/plugin-delete.feature
+++ b/features/plugin-delete.feature
@@ -47,3 +47,13 @@ Feature: Delete WordPress plugins
       Success: No plugins deleted.
       """
     And the return code should be 0
+
+  Scenario: Excluding a missing plugin should not throw an error
+    Given a WP install
+    And I run `wp plugin delete --all --exclude=missing-plugin`
+    Then STDERR should be empty
+    And STDOUT should contain:
+      """
+      Success:
+      """
+    And the return code should be 0
diff --git a/features/plugin-uninstall.feature b/features/plugin-uninstall.feature
index 86ef9dbe..e267507b 100644
--- a/features/plugin-uninstall.feature
+++ b/features/plugin-uninstall.feature
@@ -79,3 +79,15 @@ Feature: Uninstall a WordPress plugin
       Success: No plugins uninstalled.
       """
     And the return code should be 0
+
+
+
+  Scenario: Excluding a missing plugin should not throw an error
+    Given a WP install
+    And I run `wp plugin uninstall --all --exclude=missing-plugin`
+    Then STDERR should be empty
+    And STDOUT should contain:
+      """
+      Success:
+      """
+    And the return code should be 0
diff --git a/features/plugin-update.feature b/features/plugin-update.feature
index 1a884135..1aa586b7 100644
--- a/features/plugin-update.feature
+++ b/features/plugin-update.feature
@@ -218,3 +218,13 @@ Feature: Update WordPress plugins
       """
       Success:
       """
+
+  Scenario: Excluding a missing plugin should not throw an error
+    Given a WP install
+    And I run `wp plugin update --all --exclude=missing-plugin`
+    Then STDERR should be empty
+    And STDOUT should contain:
+      """
+      Success:
+      """
+    And the return code should be 0
diff --git a/features/theme.feature b/features/theme.feature
index 660452d5..470bed9c 100644
--- a/features/theme.feature
+++ b/features/theme.feature
@@ -673,3 +673,15 @@ Feature: Manage WordPress themes
 
     When I try `wp theme is-active p2`
     Then the return code should be 1
+
+  Scenario: Excluding a missing theme should not throw an error
+    Given a WP install
+    And I run `wp theme delete --all --force`
+    And I run `wp theme install p2 --version=1.5.5 --activate`
+    And I run `wp theme update --all --exclude=missing-theme`
+    Then STDERR should be empty
+    And STDOUT should contain:
+      """
+      Success:
+      """
+    And the return code should be 0
diff --git a/src/WP_CLI/CommandWithUpgrade.php b/src/WP_CLI/CommandWithUpgrade.php
index 27f4a3ec..b95cf4f6 100755
--- a/src/WP_CLI/CommandWithUpgrade.php
+++ b/src/WP_CLI/CommandWithUpgrade.php
@@ -360,9 +360,15 @@ protected function update_many( $args, $assoc_args ) {
 			foreach ( $exclude_items as $item ) {
 				if ( 'plugin' === $this->item_type ) {
 					$plugin = $this->fetcher->get( $item );
+					if ( ! $plugin ) {
+						continue;
+					}
 					unset( $items_to_update[ $plugin->file ] );
 				} elseif ( 'theme' === $this->item_type ) {
 					$theme_root = get_theme_root() . '/' . $item;
+					if ( ! is_dir( $theme_root ) ) {
+						continue;
+					}
 					unset( $items_to_update[ $theme_root ] );
 				}
 			}