diff --git a/src/Configurator/DockerComposeConfigurator.php b/src/Configurator/DockerComposeConfigurator.php
index e1f07c33..84b8afd2 100644
--- a/src/Configurator/DockerComposeConfigurator.php
+++ b/src/Configurator/DockerComposeConfigurator.php
@@ -277,6 +277,13 @@ private function configureDockerCompose(Recipe $recipe, array $config, bool $upd
                 // Keep end in memory (check break line on previous line)
                 if (null !== $node) {
                     $endAt[$node] = !$i || '' !== trim($lines[$i - 1]) ? $i : $i - 1;
+                    // Prune nodesLines[old node] to match the range the splice will replace.
+                    if (isset($nodesLines[$node][$i])) {
+                        unset($nodesLines[$node][$i]);
+                        if ('' === trim($lines[$i - 1])) {
+                            unset($nodesLines[$node][$i - 1]);
+                        }
+                    }
                 }
                 $node = $matches[1];
                 if (!isset($nodesLines[$node])) {
@@ -307,14 +314,15 @@ private function configureDockerCompose(Recipe $recipe, array $config, bool $upd
                     array_splice($lines, $startAt[$key], $length, ltrim($updatedContents, "\n"));
 
                     // reset any start/end positions after this to the new positions
+                    $shift = $length - 1;
                     foreach ($startAt as $sectionKey => $at) {
                         if ($at > $originalEndAt) {
-                            $startAt[$sectionKey] = $at - $length - 1;
+                            $startAt[$sectionKey] = $at - $shift;
                         }
                     }
                     foreach ($endAt as $sectionKey => $at) {
                         if ($at > $originalEndAt) {
-                            $endAt[$sectionKey] = $at - $length;
+                            $endAt[$sectionKey] = $at - $shift;
                         }
                     }
 
diff --git a/tests/Configurator/DockerComposeConfiguratorTest.php b/tests/Configurator/DockerComposeConfiguratorTest.php
index 7c2dec88..efaa9f32 100644
--- a/tests/Configurator/DockerComposeConfiguratorTest.php
+++ b/tests/Configurator/DockerComposeConfiguratorTest.php
@@ -209,6 +209,29 @@ public function testConfigure(string $fileName)
         $this->assertEquals(self::ORIGINAL_CONTENT, file_get_contents($dockerComposeFile));
     }
 
+    public function testReconfigureDoesNotDuplicateLaterTopLevelKey()
+    {
+        $this->configurator->configure($this->recipeDb, self::CONFIG_DB, $this->lock);
+
+        $servicesOnlyRecipe = $this->getMockBuilder(Recipe::class)->disableOriginalConstructor()->getMock();
+        $servicesOnlyRecipe->method('getName')->willReturn('acme/services-only');
+        $servicesOnlyConfig = [
+            'services' => [
+                'cache:',
+                '  image: redis:alpine',
+            ],
+        ];
+
+        $this->configurator->configure($servicesOnlyRecipe, $servicesOnlyConfig, $this->lock);
+        $afterFirstConfigure = file_get_contents(FLEX_TEST_DIR.'/compose.yaml');
+
+        $this->configurator->configure($servicesOnlyRecipe, $servicesOnlyConfig, $this->lock, ['force' => true]);
+        $afterSecondConfigure = file_get_contents(FLEX_TEST_DIR.'/compose.yaml');
+
+        $this->assertSame(1, substr_count($afterSecondConfigure, "\nvolumes:\n"), 'compose.yaml must contain exactly one top-level "volumes:" key');
+        $this->assertSame($afterFirstConfigure, $afterSecondConfigure, 'configure must be idempotent when re-run');
+    }
+
     public function testNotConfiguredIfConfigSet()
     {
         $this->package->setExtra(['symfony' => ['docker' => false]]);