diff --git a/paper-api/src/main/java/org/bukkit/configuration/file/YamlConfiguration.java b/paper-api/src/main/java/org/bukkit/configuration/file/YamlConfiguration.java
index be8d35f156..6476f3794b 100644
--- a/paper-api/src/main/java/org/bukkit/configuration/file/YamlConfiguration.java
+++ b/paper-api/src/main/java/org/bukkit/configuration/file/YamlConfiguration.java
@@ -66,6 +66,8 @@ public class YamlConfiguration extends FileConfiguration {
             options().header(header);
         }
 
+        this.map.clear();
+
         if (input != null) {
             convertMapsToSections(input, this);
         }
diff --git a/paper-api/src/test/java/org/bukkit/configuration/file/FileConfigurationTest.java b/paper-api/src/test/java/org/bukkit/configuration/file/FileConfigurationTest.java
index a996753b93..4ef7aa9818 100644
--- a/paper-api/src/test/java/org/bukkit/configuration/file/FileConfigurationTest.java
+++ b/paper-api/src/test/java/org/bukkit/configuration/file/FileConfigurationTest.java
@@ -206,4 +206,69 @@ public abstract class FileConfigurationTest extends MemoryConfigurationTest {
 
         assertEquals("", config.saveToString());
     }
+
+    @Test
+    public void testReloadClear() throws Exception {
+        // Test for SPIGOT-6274 - load does not clear values
+        FileConfiguration config = getConfig();
+
+        assertFalse(config.contains("test"));
+        assertFalse(config.getBoolean("test"));
+
+        config.set("test", true);
+        assertTrue(config.contains("test"));
+        assertTrue(config.getBoolean("test"));
+
+        config.loadFromString("");
+        assertFalse(config.contains("test"));
+        assertFalse(config.getBoolean("test"));
+
+        assertFalse(config.contains("test"));
+        assertFalse(config.getBoolean("test"));
+    }
+
+    @Test
+    public void testReloadClear2() throws Exception {
+        // Test for SPIGOT-6274 - load does not clear values
+        FileConfiguration config = getConfig();
+
+        assertFalse(config.contains("test"));
+        assertFalse(config.getBoolean("test"));
+
+        config.set("test", true);
+        assertTrue(config.contains("test"));
+        assertTrue(config.getBoolean("test"));
+
+        config.loadFromString("other: false"); // Test both null and non-null code paths
+        assertFalse(config.contains("test"));
+        assertFalse(config.getBoolean("test"));
+
+        assertFalse(config.contains("test"));
+        assertFalse(config.getBoolean("test"));
+    }
+
+    @Test
+    public void testReloadClear3() throws Exception {
+        // Test for SPIGOT-6274 - load does not clear values
+        FileConfiguration config = getConfig();
+
+        assertFalse(config.contains("test"));
+        assertFalse(config.getBoolean("test"));
+
+        config.set("test", true);
+        assertTrue(config.contains("test"));
+        assertTrue(config.getBoolean("test"));
+
+        config.loadFromString("other: false\nsection:\n  value: true"); // SPIGOT-6313: Test with section
+        assertFalse(config.contains("test"));
+        assertFalse(config.getBoolean("test"));
+
+        assertTrue(config.contains("other"));
+        assertTrue(config.contains("section"));
+        assertTrue(config.contains("section.value"));
+        assertTrue(config.getBoolean("section.value"));
+
+        assertFalse(config.contains("test"));
+        assertFalse(config.getBoolean("test"));
+    }
 }