diff --git a/src/chocolatey.console/Program.cs b/src/chocolatey.console/Program.cs
index 5cb43e8ff4..2250280427 100644
--- a/src/chocolatey.console/Program.cs
+++ b/src/chocolatey.console/Program.cs
@@ -82,8 +82,6 @@ that chocolatey.licensed.dll exists at
                 }
                 var container = SimpleInjectorContainer.Container;
 
-                add_or_remove_licensed_source(license, container);
-
                 var config = container.GetInstance<ChocolateyConfiguration>();
                 var fileSystem = container.GetInstance<IFileSystem>();
 
@@ -224,37 +222,6 @@ private static void remove_old_chocolatey_exe(IFileSystem fileSystem)
             }
         }
 
-        private static void add_or_remove_licensed_source(ChocolateyLicense license, Container container)
-        {
-            var addOrUpdate = license.IsValid;
-            var config = new ChocolateyConfiguration {
-                    RegularOutput = false,
-                    QuietOutput = true,
-                };
-
-            var sourceService = container.GetInstance<IChocolateyConfigSettingsService>();
-            var sources = sourceService.source_list(config);
-
-            config.SourceCommand.Name = ApplicationParameters.ChocolateyLicensedFeedSourceName;
-            config.Sources = ApplicationParameters.ChocolateyLicensedFeedSource;
-            config.SourceCommand.Username = "customer";
-            config.SourceCommand.Password = license.Id;
-            config.SourceCommand.Priority = 10;
-
-            if (addOrUpdate && !sources.Any(s => 
-                    s.Id.is_equal_to(ApplicationParameters.ChocolateyLicensedFeedSourceName)
-                    && s.Authenticated)
-                )
-            {
-                sourceService.source_add(config);
-            }
-
-            if (!addOrUpdate)
-            {
-                sourceService.source_remove(config);
-            }
-        }
-
         private static void pause_execution_if_debug()
         {
 #if DEBUG
diff --git a/src/chocolatey/infrastructure.app/builders/ConfigurationBuilder.cs b/src/chocolatey/infrastructure.app/builders/ConfigurationBuilder.cs
index 63291deb24..3a50ac18a2 100644
--- a/src/chocolatey/infrastructure.app/builders/ConfigurationBuilder.cs
+++ b/src/chocolatey/infrastructure.app/builders/ConfigurationBuilder.cs
@@ -70,6 +70,8 @@ public static void set_up_configuration(IList<string> args, ChocolateyConfigurat
             var fileSystem = container.GetInstance<IFileSystem>();
             var xmlService = container.GetInstance<IXmlService>();
             var configFileSettings = get_config_file_settings(fileSystem, xmlService);
+            // must be done prior to setting the file configuration
+            add_or_remove_licensed_source(license, configFileSettings);
             set_file_configuration(config, configFileSettings, fileSystem, notifyWarnLoggingAction);
             ConfigurationOptions.reset_options();
             set_global_options(args, config, container);
@@ -77,6 +79,7 @@ public static void set_up_configuration(IList<string> args, ChocolateyConfigurat
             set_environment_variables(config);
             // must be done last for overrides
             set_licensed_options(config, license, configFileSettings);
+            // save all changes if there are any
             set_config_file_settings(configFileSettings, xmlService);
         }
 
@@ -98,6 +101,36 @@ private static void set_config_file_settings(ConfigFileSettings configFileSettin
                 logWarningInsteadOfError: true);
         }
 
+        private static void add_or_remove_licensed_source(ChocolateyLicense license, ConfigFileSettings configFileSettings)
+        {
+            // do not enable or disable the source, in case the user has disabled it
+            var addOrUpdate = license.IsValid;
+            var sources = configFileSettings.Sources.Where(s => !s.Disabled).or_empty_list_if_null().ToList();
+
+            var configSource = new ConfigFileSourceSetting
+            {
+                Id = ApplicationParameters.ChocolateyLicensedFeedSourceName,
+                Value = ApplicationParameters.ChocolateyLicensedFeedSource,
+                UserName = "customer",
+                Password = NugetEncryptionUtility.EncryptString(license.Id),
+                Priority = 10
+            };
+
+            if (addOrUpdate && !sources.Any(s =>
+                    s.Id.is_equal_to(ApplicationParameters.ChocolateyLicensedFeedSourceName)
+                    && NugetEncryptionUtility.DecryptString(s.Password).is_equal_to(license.Id)
+                    )
+                )
+            {
+                configFileSettings.Sources.Add(configSource);
+            }
+
+            if (!addOrUpdate)
+            {
+                configFileSettings.Sources.RemoveWhere(s => s.Id.is_equal_to(configSource.Id));
+            }
+        }
+
         private static void set_file_configuration(ChocolateyConfiguration config, ConfigFileSettings configFileSettings, IFileSystem fileSystem, Action<string> notifyWarnLoggingAction)
         {
             var sources = new StringBuilder();