diff --git a/core/src/main/java/org/elasticsearch/common/settings/Settings.java b/core/src/main/java/org/elasticsearch/common/settings/Settings.java
index 374d923d30a37..b4ab00267c524 100644
--- a/core/src/main/java/org/elasticsearch/common/settings/Settings.java
+++ b/core/src/main/java/org/elasticsearch/common/settings/Settings.java
@@ -57,6 +57,7 @@
 import java.util.Iterator;
 import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.NoSuchElementException;
 import java.util.Objects;
@@ -442,6 +443,20 @@ public String[] getAsArray(String settingPrefix, String[] defaultArray) throws S
     public String[] getAsArray(String settingPrefix, String[] defaultArray, Boolean commaDelimited) throws SettingsException {
         List<String> result = new ArrayList<>();
 
+        final String valueFromPrefix = get(settingPrefix);
+        final String valueFromPreifx0 = get(settingPrefix + ".0");
+
+        if (valueFromPrefix != null && valueFromPreifx0 != null) {
+            final String message = String.format(
+                    Locale.ROOT,
+                    "settings object contains values for [%s=%s] and [%s=%s]",
+                    settingPrefix,
+                    valueFromPrefix,
+                    settingPrefix + ".0",
+                    valueFromPreifx0);
+            throw new IllegalStateException(message);
+        }
+
         if (get(settingPrefix) != null) {
             if (commaDelimited) {
                 String[] strings = Strings.splitStringByCommaToArray(get(settingPrefix));
diff --git a/core/src/main/java/org/elasticsearch/node/InternalSettingsPreparer.java b/core/src/main/java/org/elasticsearch/node/InternalSettingsPreparer.java
index f5501437bcc46..5261268bd4bd3 100644
--- a/core/src/main/java/org/elasticsearch/node/InternalSettingsPreparer.java
+++ b/core/src/main/java/org/elasticsearch/node/InternalSettingsPreparer.java
@@ -125,14 +125,21 @@ public static Environment prepareEnvironment(Settings input, Terminal terminal,
     }
 
     /**
-     * Initializes the builder with the given input settings, and loads system properties settings if allowed.
-     * If loadDefaults is true, system property default settings are loaded.
+     * Initializes the builder with the given input settings, and applies settings and default settings from the specified map (these
+     * settings typically come from the command line). The default settings are applied only if the setting does not exist in the specified
+     * output.
+     *
+     * @param output the settings builder to apply the input and default settings to
+     * @param input the input settings
+     * @param esSettings a map from which to apply settings and default settings
      */
-    private static void initializeSettings(Settings.Builder output, Settings input, Map<String, String> esSettings) {
+    static void initializeSettings(final Settings.Builder output, final Settings input, final Map<String, String> esSettings) {
         output.put(input);
         output.putProperties(esSettings,
-            PROPERTY_DEFAULTS_PREDICATE.and(key -> output.get(STRIP_PROPERTY_DEFAULTS_PREFIX.apply(key)) == null),
-            STRIP_PROPERTY_DEFAULTS_PREFIX);
+                PROPERTY_DEFAULTS_PREDICATE
+                        .and(key -> output.get(STRIP_PROPERTY_DEFAULTS_PREFIX.apply(key)) == null)
+                        .and(key -> output.get(STRIP_PROPERTY_DEFAULTS_PREFIX.apply(key) + ".0") == null),
+                STRIP_PROPERTY_DEFAULTS_PREFIX);
         output.putProperties(esSettings, PROPERTY_DEFAULTS_PREDICATE.negate(), Function.identity());
         output.replacePropertyPlaceholders();
     }
diff --git a/core/src/test/java/org/elasticsearch/common/settings/SettingsTests.java b/core/src/test/java/org/elasticsearch/common/settings/SettingsTests.java
index c1dc07116ecf1..6eec34a90e981 100644
--- a/core/src/test/java/org/elasticsearch/common/settings/SettingsTests.java
+++ b/core/src/test/java/org/elasticsearch/common/settings/SettingsTests.java
@@ -562,4 +562,16 @@ public void testSecureSettingConflict() {
         IllegalArgumentException e = expectThrows(IllegalArgumentException.class, () -> setting.get(settings));
         assertTrue(e.getMessage().contains("must be stored inside the Elasticsearch keystore"));
     }
+
+    public void testGetAsArrayFailsOnDuplicates() {
+        final Settings settings =
+                Settings.builder()
+                        .put("foobar.0", "bar")
+                        .put("foobar.1", "baz")
+                        .put("foobar", "foo")
+                        .build();
+        final IllegalStateException e = expectThrows(IllegalStateException.class, () -> settings.getAsArray("foobar"));
+        assertThat(e, hasToString(containsString("settings object contains values for [foobar=foo] and [foobar.0=bar]")));
+    }
+
 }
diff --git a/core/src/test/java/org/elasticsearch/node/internal/InternalSettingsPreparerTests.java b/core/src/test/java/org/elasticsearch/node/InternalSettingsPreparerTests.java
similarity index 93%
rename from core/src/test/java/org/elasticsearch/node/internal/InternalSettingsPreparerTests.java
rename to core/src/test/java/org/elasticsearch/node/InternalSettingsPreparerTests.java
index daaeab8014369..44c4b880fb68f 100644
--- a/core/src/test/java/org/elasticsearch/node/internal/InternalSettingsPreparerTests.java
+++ b/core/src/test/java/org/elasticsearch/node/InternalSettingsPreparerTests.java
@@ -17,7 +17,7 @@
  * under the License.
  */
 
-package org.elasticsearch.node.internal;
+package org.elasticsearch.node;
 
 import org.elasticsearch.cli.MockTerminal;
 import org.elasticsearch.cluster.ClusterName;
@@ -196,4 +196,15 @@ public void testDefaultPropertiesOverride() throws Exception {
         Environment env = InternalSettingsPreparer.prepareEnvironment(baseEnvSettings, null, props);
         assertEquals("bar", env.settings().get("setting"));
     }
+
+    public void testDefaultWithArray() {
+        final Settings.Builder output = Settings.builder().put("foobar.0", "bar").put("foobar.1", "baz");
+        final Map<String, String> esSettings = Collections.singletonMap("default.foobar", "foo");
+        InternalSettingsPreparer.initializeSettings(output, Settings.EMPTY, esSettings);
+        final Settings settings = output.build();
+        assertThat(settings.get("foobar.0"), equalTo("bar"));
+        assertThat(settings.get("foobar.1"), equalTo("baz"));
+        assertNull(settings.get("foobar"));
+    }
+
 }