diff --git a/paper-server/src/main/java/io/papermc/paper/configuration/PaperConfigurations.java b/paper-server/src/main/java/io/papermc/paper/configuration/PaperConfigurations.java
index e48fa405d..266932720 100644
--- a/paper-server/src/main/java/io/papermc/paper/configuration/PaperConfigurations.java
+++ b/paper-server/src/main/java/io/papermc/paper/configuration/PaperConfigurations.java
@@ -101,6 +101,7 @@ public class PaperConfigurations extends Configurations<GlobalConfiguration, Wor
             The world configuration options have been moved inside
             their respective world folder. The files are named %s
 
+            File Reference: https://docs.papermc.io/paper/reference/global-configuration/
             Docs: https://docs.papermc.io/
             Discord: https://discord.gg/papermc
             Website: https://papermc.io/""", WORLD_CONFIG_FILE_NAME);
@@ -116,6 +117,7 @@ public class PaperConfigurations extends Configurations<GlobalConfiguration, Wor
             Configuration options here apply to all worlds, unless you specify overrides inside
             the world-specific config file inside each world folder.
 
+            File Reference: https://docs.papermc.io/paper/reference/world-configuration/
             Docs: https://docs.papermc.io/
             Discord: https://discord.gg/papermc
             Website: https://papermc.io/""";
@@ -124,6 +126,8 @@ public class PaperConfigurations extends Configurations<GlobalConfiguration, Wor
         This is a world configuration file for Paper.
         This file may start empty but can be filled with settings to override ones in the %s/%s
         
+        For more information, see https://docs.papermc.io/paper/reference/configuration/#per-world-configuration
+        
         World: %s (%s)""",
         PaperConfigurations.CONFIG_DIR,
         PaperConfigurations.WORLD_DEFAULTS_CONFIG_FILE_NAME,
diff --git a/paper-server/src/main/java/org/bukkit/craftbukkit/CraftServer.java b/paper-server/src/main/java/org/bukkit/craftbukkit/CraftServer.java
index ab781cb77..71f7a8386 100644
--- a/paper-server/src/main/java/org/bukkit/craftbukkit/CraftServer.java
+++ b/paper-server/src/main/java/org/bukkit/craftbukkit/CraftServer.java
@@ -432,7 +432,9 @@ public final class CraftServer implements Server {
 
         this.configuration = YamlConfiguration.loadConfiguration(this.getConfigFile());
         this.configuration.options().copyDefaults(true);
-        this.configuration.setDefaults(YamlConfiguration.loadConfiguration(new InputStreamReader(this.getClass().getClassLoader().getResourceAsStream("configurations/bukkit.yml"), StandardCharsets.UTF_8)));
+        YamlConfiguration configurationDefaults = YamlConfiguration.loadConfiguration(new InputStreamReader(this.getClass().getClassLoader().getResourceAsStream("configurations/bukkit.yml"), StandardCharsets.UTF_8));
+        this.configuration.setDefaults(configurationDefaults);
+        this.configuration.options().setHeader(configurationDefaults.options().getHeader());
         ConfigurationSection legacyAlias = null;
         if (!this.configuration.isString("aliases")) {
             legacyAlias = this.configuration.getConfigurationSection("aliases");
@@ -449,6 +451,7 @@ public final class CraftServer implements Server {
         if (this.commandsConfiguration.contains("aliases")) commandsDefaults.set("aliases", null);
         this.commandsConfiguration.setDefaults(commandsDefaults);
         // Paper end - don't enforce icanhasbukkit default if alias block exists
+        this.commandsConfiguration.options().setHeader(commandsDefaults.options().getHeader());
         this.saveCommandsConfig();
 
         // Migrate aliases from old file and add previously implicit $1- to pass all arguments
diff --git a/paper-server/src/main/java/org/bukkit/craftbukkit/help/HelpYamlReader.java b/paper-server/src/main/java/org/bukkit/craftbukkit/help/HelpYamlReader.java
index bbaeb00af..b345a4973 100644
--- a/paper-server/src/main/java/org/bukkit/craftbukkit/help/HelpYamlReader.java
+++ b/paper-server/src/main/java/org/bukkit/craftbukkit/help/HelpYamlReader.java
@@ -32,11 +32,10 @@ public class HelpYamlReader {
             this.helpYaml = YamlConfiguration.loadConfiguration(helpYamlFile);
             this.helpYaml.options().copyDefaults(true);
             this.helpYaml.setDefaults(defaultConfig);
+            this.helpYaml.options().setHeader(defaultConfig.options().getHeader());
 
             try {
-                if (!helpYamlFile.exists()) {
-                    this.helpYaml.save(helpYamlFile);
-                }
+                this.helpYaml.save(helpYamlFile);
             } catch (IOException ex) {
                 server.getLogger().log(Level.SEVERE, "Could not save " + helpYamlFile, ex);
             }
diff --git a/paper-server/src/main/java/org/spigotmc/SpigotConfig.java b/paper-server/src/main/java/org/spigotmc/SpigotConfig.java
index c935d75b8..ba539e6a3 100644
--- a/paper-server/src/main/java/org/spigotmc/SpigotConfig.java
+++ b/paper-server/src/main/java/org/spigotmc/SpigotConfig.java
@@ -33,17 +33,17 @@ public class SpigotConfig {
 
     private static File CONFIG_FILE;
     private static final String HEADER = """
-        This is the main configuration file for Spigot.
+        This is the Spigot configuration file for Paper.
         As you can see, there's tons to configure. Some options may impact gameplay, so use
         with caution, and make sure you know what each option does before configuring.
-        For a reference for any variable inside this file, check out the Spigot wiki at
-        http://www.spigotmc.org/wiki/spigot-configuration/
         
-        If you need help with the configuration or have any questions related to Spigot,
-        join us at the Discord or drop by our forums and leave a post.
+        If you need help with the configuration or have any questions related to Paper,
+        join us in our Discord or check the docs page.
         
-        Discord: https://www.spigotmc.org/go/discord
-        Forums: http://www.spigotmc.org/
+        File Reference: https://docs.papermc.io/paper/reference/spigot-configuration/
+        Docs: https://docs.papermc.io/
+        Discord: https://discord.gg/papermc
+        Website: https://papermc.io/
         """;
     /*========================================================================*/
     public static YamlConfiguration config;
diff --git a/paper-server/src/main/resources/configurations/bukkit.yml b/paper-server/src/main/resources/configurations/bukkit.yml
index eef7c125b..00a5b4dc0 100644
--- a/paper-server/src/main/resources/configurations/bukkit.yml
+++ b/paper-server/src/main/resources/configurations/bukkit.yml
@@ -1,15 +1,13 @@
-# This is the main configuration file for Bukkit.
+# This is the Bukkit configuration file in Paper.
 # As you can see, there's actually not that much to configure without any plugins.
-# For a reference for any variable inside this file, check out the Bukkit Wiki at
-# https://www.spigotmc.org/go/bukkit-yml
-# 
-# If you need help on this file, feel free to join us on Discord or leave a message
-# on the forums asking for advice.
-# 
-# Discord: https://www.spigotmc.org/go/discord
-# Forums: https://www.spigotmc.org/
-# Bug tracker: https://www.spigotmc.org/go/bugs
-
+#
+# If you need help with the configuration or have any questions related to Paper,
+# join us in our Discord or check the docs page.
+#
+# File Reference: https://docs.papermc.io/paper/reference/bukkit-configuration/
+# Docs: https://docs.papermc.io/
+# Discord: https://discord.gg/papermc
+# Website: https://papermc.io/
 
 settings:
     allow-end: true
diff --git a/paper-server/src/main/resources/configurations/commands.yml b/paper-server/src/main/resources/configurations/commands.yml
index 18f545712..ddf2cd4b8 100644
--- a/paper-server/src/main/resources/configurations/commands.yml
+++ b/paper-server/src/main/resources/configurations/commands.yml
@@ -1,13 +1,12 @@
-# This is the commands configuration file for Bukkit.
-# For documentation on how to make use of this file, check out the Bukkit Wiki at
-# https://www.spigotmc.org/go/commands-yml
-# 
-# If you need help on this file, feel free to join us on Discord or leave a message
-# on the forums asking for advice.
-# 
-# Discord: https://www.spigotmc.org/go/discord
-# Forums: https://www.spigotmc.org/
-# Bug tracker: https://www.spigotmc.org/go/bugs
+# This is the Bukkit commands configuration file for Paper.
+#
+# If you need help with the configuration or have any questions related to Paper,
+# join us in our Discord or check the docs page.
+#
+# File Reference: https://docs.papermc.io/paper/reference/bukkit-commands-configuration/
+# Docs: https://docs.papermc.io/
+# Discord: https://discord.gg/papermc
+# Website: https://papermc.io/
 
 command-block-overrides: []
 ignore-vanilla-permissions: false
diff --git a/paper-server/src/main/resources/configurations/help.yml b/paper-server/src/main/resources/configurations/help.yml
index 15c3d0707..2cd6b353e 100644
--- a/paper-server/src/main/resources/configurations/help.yml
+++ b/paper-server/src/main/resources/configurations/help.yml
@@ -1,4 +1,4 @@
-# This is the help configuration file for Bukkit.
+# This is the Bukkit help configuration file for Paper.
 # 
 # By default you do not need to modify this file. Help topics for all plugin commands are automatically provided by
 # or extracted from your installed plugins. You only need to modify this file if you wish to add new help pages to
@@ -53,3 +53,10 @@
 #    - PluginNameOne
 #    - PluginNameTwo
 #    - PluginNameThree
+#
+# If you need help with the configuration or have any questions related to Paper,
+# join us in our Discord or check the docs page.
+#
+# Docs: https://docs.papermc.io/
+# Discord: https://discord.gg/papermc
+# Website: https://papermc.io/