diff --git a/src/Database/Query.php b/src/Database/Query.php
index 51884f40995..989ef62285a 100644
--- a/src/Database/Query.php
+++ b/src/Database/Query.php
@@ -659,6 +659,7 @@ public function join($tables = null, $types = [], $overwrite = false) {
 
 		$types += $this->defaultTypes();
 		$joins = [];
+		$i = count($this->_parts['join']);
 		foreach ($tables as $alias => $t) {
 			if (!is_array($t)) {
 				$t = ['table' => $t, 'conditions' => $this->newExpr()];
@@ -666,13 +667,14 @@ public function join($tables = null, $types = [], $overwrite = false) {
 			if (!($t['conditions']) instanceof ExpressionInterface) {
 				$t['conditions'] = $this->newExpr()->add($t['conditions'], $types);
 			}
-			$joins[] = $t + ['type' => 'INNER', 'alias' => is_string($alias) ? $alias : null];
+			$alias = is_string($alias) ? $alias : null;
+			$joins[$alias ?: $i++] = $t + ['type' => 'INNER', 'alias' => $alias];
 		}
 
 		if ($overwrite) {
 			$this->_parts['join'] = $joins;
 		} else {
-			$this->_parts['join'] = array_merge($this->_parts['join'], array_values($joins));
+			$this->_parts['join'] = array_merge($this->_parts['join'], $joins);
 		}
 
 		$this->_dirty();
diff --git a/tests/TestCase/ORM/Association/BelongsToManyTest.php b/tests/TestCase/ORM/Association/BelongsToManyTest.php
index a3fc50d315b..1a586c3524d 100644
--- a/tests/TestCase/ORM/Association/BelongsToManyTest.php
+++ b/tests/TestCase/ORM/Association/BelongsToManyTest.php
@@ -703,7 +703,7 @@ public function testEagerLoaderSubquery() {
 
 		$expected = clone $parent;
 		$joins = $expected->join();
-		unset($joins[1]);
+		unset($joins['bar']);
 		$expected
 			->contain([], true)
 			->select(['Articles__id' => 'Articles.id'], true)
diff --git a/tests/TestCase/ORM/Association/HasManyTest.php b/tests/TestCase/ORM/Association/HasManyTest.php
index e6ec7b4ab82..af5c9025d9d 100644
--- a/tests/TestCase/ORM/Association/HasManyTest.php
+++ b/tests/TestCase/ORM/Association/HasManyTest.php
@@ -335,7 +335,7 @@ public function testEagerLoaderSubquery() {
 
 		$expected = clone $parent;
 		$joins = $expected->join();
-		unset($joins[1]);
+		unset($joins['bar']);
 		$expected
 			->contain([], true)
 			->select(['Authors__id' => 'Authors.id'], true)
diff --git a/tests/TestCase/ORM/QueryTest.php b/tests/TestCase/ORM/QueryTest.php
index bde1fcccf33..717dc673b85 100644
--- a/tests/TestCase/ORM/QueryTest.php
+++ b/tests/TestCase/ORM/QueryTest.php
@@ -999,7 +999,7 @@ public function testApplyOptions() {
 		$expected = new QueryExpression(['a > b']);
 		$result = $query->clause('join');
 		$this->assertEquals([
-			['alias' => 'table_a', 'type' => 'INNER', 'conditions' => $expected]
+			'table_a' => ['alias' => 'table_a', 'type' => 'INNER', 'conditions' => $expected]
 		], $result);
 
 		$expected = new OrderByExpression(['a' => 'ASC']);
@@ -1818,4 +1818,23 @@ public function testQueryWithStackedFormatters() {
 		$this->assertEquals($expected, $query->toArray());
 	}
 
+/**
+ * Tests that getting results from a query having a contained association
+ * will no attach joins twice if count() is called on it afterwards
+ *
+ * @return void
+ */
+	public function testCountWithContainCallingAll() {
+		$table = TableRegistry::get('articles');
+		$table->belongsTo('authors');
+		$query = $table->find()
+			->select(['id', 'title'])
+			->contain('authors')
+			->limit(2);
+
+		$results = $query->all();
+		$this->assertCount(2, $results);
+		$this->assertEquals(3, $query->count());
+	}
+
 }