diff --git a/src/js/_enqueues/wp/updates.js b/src/js/_enqueues/wp/updates.js
index 9f3b80b843d46..458da2de79f47 100644
--- a/src/js/_enqueues/wp/updates.js
+++ b/src/js/_enqueues/wp/updates.js
@@ -1379,6 +1379,16 @@
 				 * @type {Object}
 				 */
 				plugins          = settings.plugins,
+				/**
+				 * Plugin groups that Core handles on its own.
+				 *
+				 * @type {Array}
+				 */
+				coreGroups       = [
+					'all', 'search', 'upgrade', 'active', 'inactive',
+					'recently_activated', 'mustuse', 'dropins', 'paused',
+					'auto-update-enabled', 'auto-update-disabled'
+				],
 				remainingCount;
 
 			// Add a success message after deleting a plugin.
@@ -1447,6 +1457,24 @@
 				}
 			}
 
+			// Remove from custom groups added through the `plugins_list` filter.
+			_.each( _.keys( plugins ), function( group ) {
+				var $view;
+
+				if ( -1 !== _.indexOf( coreGroups, group ) || ! _.isArray( plugins[ group ] ) || -1 === _.indexOf( plugins[ group ], response.plugin ) ) {
+					return;
+				}
+
+				plugins[ group ] = _.without( plugins[ group ], response.plugin );
+				$view = $views.children( 'li.' + $.escapeSelector( group ) );
+
+				if ( plugins[ group ].length ) {
+					$view.find( '.count' ).text( '(' + plugins[ group ].length + ')' );
+				} else {
+					$view.remove();
+				}
+			} );
+
 			plugins.all = _.without( plugins.all, response.plugin );
 
 			if ( plugins.all.length ) {
@@ -1460,6 +1488,9 @@
 				}
 			}
 
+			// Remove the trailing separator left on the last view when the view after it was removed.
+			$views.find( 'li:last' ).html( function() { return $( this ).children(); } );
+
 			if ( $itemsCount.length && $currentView.length ) {
 				remainingCount = plugins[ $currentView.parent( 'li' ).attr('class') ].length;
 				$itemsCount.text(
diff --git a/tests/qunit/wp-admin/js/updates.js b/tests/qunit/wp-admin/js/updates.js
index 9d3948811abfd..500d74a63afed 100644
--- a/tests/qunit/wp-admin/js/updates.js
+++ b/tests/qunit/wp-admin/js/updates.js
@@ -122,6 +122,78 @@ jQuery( function( $ ) {
 		assert.equal( jQuery.ajax.getCall( 0 ).args[0].data.action, 'delete-plugin' );
 		assert.equal( jQuery.ajax.getCall( 0 ).args[0].data.slug, 'jetpack' );
 	} );
+	QUnit.test( 'Deleting a plugin should update the counts of custom plugin groups', function( assert ) {
+		var plugins = window._wpUpdatesSettings.plugins;
+
+		$( '#qunit-fixture' ).append(
+			'<script type="text/html" id="tmpl-item-deleted-row"><tr class="plugin-deleted-tr"><td colspan="{{ data.colspan }}"></td></tr></script>' +
+			'<ul class="subsubsub">' +
+				'<li class="all"><a href="#">All <span class="count">(3)</span></a> |</li>' +
+				'<li class="demo_group"><a href="#">Demo Group <span class="count">(2)</span></a> |</li>' +
+				'<li class="single_group"><a href="#">Single Group <span class="count">(1)</span></a></li>' +
+			'</ul>' +
+			'<form id="bulk-action-form"><table><tbody id="the-list">' +
+				'<tr data-plugin="custom-a/custom-a.php"><td></td></tr>' +
+			'</tbody></table></form>'
+		);
+
+		window._wpUpdatesSettings.plugins = {
+			all: [ 'custom-a/custom-a.php', 'custom-b/custom-b.php', 'other/other.php' ],
+			demo_group: [ 'custom-a/custom-a.php', 'custom-b/custom-b.php' ],
+			single_group: [ 'custom-a/custom-a.php' ]
+		};
+
+		// Run the fade out callback right away.
+		sinon.stub( $.fn, 'fadeOut' ).callsFake( function( speed, callback ) {
+			return this.each( callback );
+		} );
+
+		wp.updates.deletePluginSuccess( { slug: 'custom-a', plugin: 'custom-a/custom-a.php', pluginName: 'Custom A' } );
+
+		$.fn.fadeOut.restore();
+
+		assert.equal( $( '.subsubsub .all .count' ).text(), '(2)', 'The All count should go down.' );
+		assert.equal( $( '.subsubsub .demo_group .count' ).text(), '(1)', 'The custom group count should go down.' );
+		assert.strictEqual( $( '.subsubsub .single_group' ).length, 0, 'An empty custom group should be removed.' );
+		assert.strictEqual( $( '.subsubsub .all' ).text(), 'All (2) |', 'Separators between views should be kept.' );
+		assert.strictEqual( $( '.subsubsub .demo_group' ).text(), 'Demo Group (1)', 'The new last view should not end with a separator.' );
+		assert.deepEqual( window._wpUpdatesSettings.plugins.demo_group, [ 'custom-b/custom-b.php' ], 'The deleted plugin should be removed from the custom group.' );
+
+		window._wpUpdatesSettings.plugins = plugins;
+	} );
+	QUnit.test( 'Deleting a plugin should only remove the view of an emptied custom group', function( assert ) {
+		var plugins = window._wpUpdatesSettings.plugins;
+
+		$( '#qunit-fixture' ).append(
+			'<script type="text/html" id="tmpl-item-deleted-row"><tr class="plugin-deleted-tr"><td colspan="{{ data.colspan }}"></td></tr></script>' +
+			'<ul class="subsubsub">' +
+				'<li class="all"><a href="#">All <span class="count">(2)</span></a> |</li>' +
+				'<li class="count"><a href="#">Count <span class="count">(1)</span></a></li>' +
+			'</ul>' +
+			'<form id="bulk-action-form"><table><tbody id="the-list">' +
+				'<tr data-plugin="custom-a/custom-a.php"><td></td></tr>' +
+			'</tbody></table></form>'
+		);
+
+		// A group key that matches the class of the count elements.
+		window._wpUpdatesSettings.plugins = {
+			all: [ 'custom-a/custom-a.php', 'other/other.php' ],
+			count: [ 'custom-a/custom-a.php' ]
+		};
+
+		sinon.stub( $.fn, 'fadeOut' ).callsFake( function( speed, callback ) {
+			return this.each( callback );
+		} );
+
+		wp.updates.deletePluginSuccess( { slug: 'custom-a', plugin: 'custom-a/custom-a.php', pluginName: 'Custom A' } );
+
+		$.fn.fadeOut.restore();
+
+		assert.strictEqual( $( '.subsubsub > li.count' ).length, 0, 'The emptied group view should be removed.' );
+		assert.strictEqual( $( '.subsubsub .all' ).text(), 'All (1)', 'The All view should keep its count.' );
+
+		window._wpUpdatesSettings.plugins = plugins;
+	} );
 
 	// QUnit.test( 'A successful update changes the message?', function( assert ) {} );
 	// QUnit.test( 'A failed update changes the message?', function( assert ) {} );