diff --git a/lib/bolt/applicator.rb b/lib/bolt/applicator.rb
index eaf4d0da0e..f832fc6843 100644
--- a/lib/bolt/applicator.rb
+++ b/lib/bolt/applicator.rb
@@ -264,7 +264,7 @@ def apply_ast(raw_ast, targets, options, plan_vars = {})
 
         result_promises = targets.zip(futures).flat_map do |target, future|
           @executor.queue_execute([target]) do |transport, batch|
-            @executor.with_node_logging("Applying manifest block", batch) do
+            @executor.with_node_logging("Applying manifest block%s" % (" (with agent confdir)" if options[:agent]), batch) do
               catalog = future.value
               if future.rejected?
                 batch.map do |batch_target|
@@ -285,7 +285,8 @@ def apply_ast(raw_ast, targets, options, plan_vars = {})
                   'plugins' => Puppet::Pops::Types::PSensitiveType::Sensitive.new(plugins),
                   'apply_settings' => @apply_settings,
                   '_task' => catalog_apply_task.name,
-                  '_noop' => options[:noop]
+                  '_noop' => options[:noop],
+                  '_agent' => options[:agent]
                 }
 
                 callback = proc do |event|
diff --git a/libexec/apply_catalog.rb b/libexec/apply_catalog.rb
index ccf6d62232..7542bae0b5 100755
--- a/libexec/apply_catalog.rb
+++ b/libexec/apply_catalog.rb
@@ -17,9 +17,9 @@
 puppet_root = Dir.mktmpdir
 moduledir = File.join(puppet_root, 'modules')
 Dir.mkdir(moduledir)
-cli = (Puppet::Settings::REQUIRED_APP_SETTINGS + [:rundir]).flat_map do |setting|
-  ["--#{setting}", File.join(puppet_root, setting.to_s.chomp('dir'))]
-end
+cli = (Puppet::Settings::REQUIRED_APP_SETTINGS + [:rundir]).filter_map do |setting|
+  ["--#{setting}", File.join(puppet_root, setting.to_s.chomp('dir'))] unless (args['_agent'] && setting == :confdir)
+end.flatten
 cli << '--modulepath' << moduledir
 Puppet.initialize_settings(cli)