diff --git a/CHANGELOG.asciidoc b/CHANGELOG.asciidoc
index 28b49fb98146..386d4c0fa4a6 100644
--- a/CHANGELOG.asciidoc
+++ b/CHANGELOG.asciidoc
@@ -68,6 +68,7 @@ https://github.com/elastic/beats/compare/v6.0.0-alpha2...master[Check the HEAD d
 - Add support for loading Xpack Machine Learning configurations from the modules, and added sample configurations for the Nginx module. {pull}4506[4506]
 - Add udp prospector type. {pull}4452[4452]
 - Enabled Cgo which means libc is dynamically compiled. {pull}4546[4546]
+- Add module config reloading mechanism {pull}4566[4566]
 
 *Heartbeat*
 
diff --git a/filebeat/_meta/common.reference.p2.yml b/filebeat/_meta/common.reference.p2.yml
index 2339507e3fbd..77b357ba4a2c 100644
--- a/filebeat/_meta/common.reference.p2.yml
+++ b/filebeat/_meta/common.reference.p2.yml
@@ -262,8 +262,14 @@ filebeat.prospectors:
 #filebeat.shutdown_timeout: 0
 
 # Enable filebeat config reloading
-#filebeat.config.prospectors:
-  #enabled: false
-  #path: configs/*.yml
-  #reload.enabled: true
-  #reload.period: 10s
+#filebeat.config:
+  #prospectors:
+    #enabled: false
+    #path: prospectors.d/*.yml
+    #reload.enabled: true
+    #reload.period: 10s
+  #modules:
+    #enabled: false
+    #path: modules.d/*.yml
+    #reload.enabled: true
+    #reload.period: 10s
diff --git a/filebeat/beater/filebeat.go b/filebeat/beater/filebeat.go
index 1d092288a1e7..a2f1c3fadad6 100644
--- a/filebeat/beater/filebeat.go
+++ b/filebeat/beater/filebeat.go
@@ -67,7 +67,7 @@ func New(b *beat.Beat, rawConfig *common.Config) (beat.Beater, error) {
 		}
 	}
 
-	if !config.ConfigProspector.Enabled() && !haveEnabledProspectors {
+	if !config.ConfigProspector.Enabled() && !config.ConfigModules.Enabled() && !haveEnabledProspectors {
 		if !b.InSetupCmd {
 			return nil, errors.New("No modules or prospectors enabled and configuration reloading disabled. What files do you want me to watch?")
 		} else {
@@ -76,7 +76,7 @@ func New(b *beat.Beat, rawConfig *common.Config) (beat.Beater, error) {
 		}
 	}
 
-	if *once && config.ConfigProspector.Enabled() {
+	if *once && config.ConfigProspector.Enabled() && config.ConfigModules.Enabled() {
 		return nil, errors.New("prospector configs and -once cannot be used together")
 	}
 
@@ -176,7 +176,8 @@ func (fb *Filebeat) Run(b *beat.Beat) error {
 		return err
 	}
 
-	crawler, err := crawler.New(channel.NewOutlet(fb.done, spooler.Channel, wgEvents), config.Prospectors, fb.done, *once)
+	outlet := channel.NewOutlet(fb.done, spooler.Channel, wgEvents)
+	crawler, err := crawler.New(outlet, config.Prospectors, b.Info.Version, fb.done, *once)
 	if err != nil {
 		logp.Err("Could not init crawler: %v", err)
 		return err
@@ -218,7 +219,7 @@ func (fb *Filebeat) Run(b *beat.Beat) error {
 		spooler.Stop()
 	}()
 
-	err = crawler.Start(registrar, config.ConfigProspector)
+	err = crawler.Start(registrar, config.ConfigProspector, config.ConfigModules)
 	if err != nil {
 		crawler.Stop()
 		return err
diff --git a/filebeat/config/config.go b/filebeat/config/config.go
index e69b6b77f087..eec92518c597 100644
--- a/filebeat/config/config.go
+++ b/filebeat/config/config.go
@@ -28,6 +28,7 @@ type Config struct {
 	ShutdownTimeout  time.Duration    `config:"shutdown_timeout"`
 	Modules          []*common.Config `config:"modules"`
 	ConfigProspector *common.Config   `config:"config.prospectors"`
+	ConfigModules    *common.Config   `config:"config.modules"`
 }
 
 var (
diff --git a/filebeat/crawler/crawler.go b/filebeat/crawler/crawler.go
index 5a54784085aa..96bffe372667 100644
--- a/filebeat/crawler/crawler.go
+++ b/filebeat/crawler/crawler.go
@@ -5,6 +5,7 @@ import (
 	"sync"
 
 	"github.com/elastic/beats/filebeat/channel"
+	"github.com/elastic/beats/filebeat/fileset"
 	"github.com/elastic/beats/filebeat/input/file"
 	"github.com/elastic/beats/filebeat/prospector"
 	"github.com/elastic/beats/filebeat/registrar"
@@ -20,22 +21,24 @@ type Crawler struct {
 	wg                sync.WaitGroup
 	reloader          *cfgfile.Reloader
 	once              bool
+	beatVersion       string
 	beatDone          chan struct{}
 }
 
-func New(out channel.Outleter, prospectorConfigs []*common.Config, beatDone chan struct{}, once bool) (*Crawler, error) {
+func New(out channel.Outleter, prospectorConfigs []*common.Config, beatVersion string, beatDone chan struct{}, once bool) (*Crawler, error) {
 
 	return &Crawler{
 		out:               out,
 		prospectors:       map[uint64]*prospector.Prospector{},
 		prospectorConfigs: prospectorConfigs,
 		once:              once,
+		beatVersion:       beatVersion,
 		beatDone:          beatDone,
 	}, nil
 }
 
 // Start starts the crawler with all prospectors
-func (c *Crawler) Start(r *registrar.Registrar, configProspectors *common.Config) error {
+func (c *Crawler) Start(r *registrar.Registrar, configProspectors *common.Config, configModules *common.Config) error {
 
 	logp.Info("Loading Prospectors: %v", len(c.prospectorConfigs))
 
@@ -57,6 +60,17 @@ func (c *Crawler) Start(r *registrar.Registrar, configProspectors *common.Config
 		}()
 	}
 
+	if configModules.Enabled() {
+		logp.Beta("Loading separate prospectors is enabled.")
+
+		c.reloader = cfgfile.NewReloader(configModules)
+		// TODO add beatVersion here
+		factory := fileset.NewFactory(c.out, r, "", c.beatDone)
+		go func() {
+			c.reloader.Run(factory)
+		}()
+	}
+
 	logp.Info("Loading and starting Prospectors completed. Enabled prospectors: %v", len(c.prospectors))
 
 	return nil
diff --git a/filebeat/filebeat.reference.yml b/filebeat/filebeat.reference.yml
index d4bcf8a60a4b..816adeb4ea46 100644
--- a/filebeat/filebeat.reference.yml
+++ b/filebeat/filebeat.reference.yml
@@ -431,11 +431,17 @@ filebeat.prospectors:
 #filebeat.shutdown_timeout: 0
 
 # Enable filebeat config reloading
-#filebeat.config.prospectors:
-  #enabled: false
-  #path: configs/*.yml
-  #reload.enabled: true
-  #reload.period: 10s
+#filebeat.config:
+  #prospectors:
+    #enabled: false
+    #path: prospectors.d/*.yml
+    #reload.enabled: true
+    #reload.period: 10s
+  #modules:
+    #enabled: false
+    #path: modules.d/*.yml
+    #reload.enabled: true
+    #reload.period: 10s
 
 #================================ General ======================================
 
diff --git a/filebeat/fileset/factory.go b/filebeat/fileset/factory.go
new file mode 100644
index 000000000000..7b223f69d41e
--- /dev/null
+++ b/filebeat/fileset/factory.go
@@ -0,0 +1,86 @@
+package fileset
+
+import (
+	"github.com/elastic/beats/libbeat/cfgfile"
+	"github.com/elastic/beats/libbeat/common"
+	"github.com/elastic/beats/libbeat/logp"
+	"github.com/mitchellh/hashstructure"
+
+	"github.com/elastic/beats/filebeat/channel"
+	"github.com/elastic/beats/filebeat/prospector"
+	"github.com/elastic/beats/filebeat/registrar"
+)
+
+// Factory is a factory for registrars
+type Factory struct {
+	outlet      channel.Outleter
+	registrar   *registrar.Registrar
+	beatVersion string
+	beatDone    chan struct{}
+}
+
+// Wrap an array of prospectors and implements cfgfile.Runner interface
+type prospectorsRunner struct {
+	id          uint64
+	prospectors []*prospector.Prospector
+}
+
+// NewFactory instantiates a new Factory
+func NewFactory(outlet channel.Outleter, registrar *registrar.Registrar, beatVersion string, beatDone chan struct{}) *Factory {
+	return &Factory{
+		outlet:      outlet,
+		registrar:   registrar,
+		beatVersion: beatVersion,
+		beatDone:    beatDone,
+	}
+}
+
+// Create creates a module based on a config
+func (f *Factory) Create(c *common.Config) (cfgfile.Runner, error) {
+	// Start a registry of one module:
+	m, err := NewModuleRegistry([]*common.Config{c}, f.beatVersion)
+	if err != nil {
+		return nil, err
+	}
+
+	pConfigs, err := m.GetProspectorConfigs()
+	if err != nil {
+		return nil, err
+	}
+
+	// Hash module ID
+	var h map[string]interface{}
+	c.Unpack(&h)
+	id, err := hashstructure.Hash(h, nil)
+	if err != nil {
+		return nil, err
+	}
+
+	prospectors := make([]*prospector.Prospector, len(pConfigs))
+	for i, pConfig := range pConfigs {
+		prospectors[i], err = prospector.NewProspector(pConfig, f.outlet, f.beatDone, f.registrar.GetStates())
+		if err != nil {
+			logp.Err("Error creating prospector: %s", err)
+			return nil, err
+		}
+	}
+
+	return &prospectorsRunner{
+		id:          id,
+		prospectors: prospectors,
+	}, nil
+}
+
+func (p *prospectorsRunner) Start() {
+	for _, prospector := range p.prospectors {
+		prospector.Start()
+	}
+}
+func (p *prospectorsRunner) Stop() {
+	for _, prospector := range p.prospectors {
+		prospector.Stop()
+	}
+}
+func (p *prospectorsRunner) ID() uint64 {
+	return p.id
+}
diff --git a/filebeat/tests/system/config/filebeat.yml.j2 b/filebeat/tests/system/config/filebeat.yml.j2
index cfe5fb64d54c..4961a452cf98 100644
--- a/filebeat/tests/system/config/filebeat.yml.j2
+++ b/filebeat/tests/system/config/filebeat.yml.j2
@@ -98,7 +98,7 @@ filebeat.registry_file: {{ beat.working_dir + '/' }}{{ registryFile|default("reg
 filebeat.publish_async: {{publish_async}}
 
 {% if reload or reload_path -%}
-filebeat.config.prospectors:
+filebeat.config.{{ reload_type|default("prospectors") }}:
   enabled: true
   path: {{ reload_path }}
   {% if reload  -%}
diff --git a/filebeat/tests/system/module/test/test/config/test.yml b/filebeat/tests/system/module/test/test/config/test.yml
new file mode 100644
index 000000000000..21548bbaf93d
--- /dev/null
+++ b/filebeat/tests/system/module/test/test/config/test.yml
@@ -0,0 +1,5 @@
+type: log
+paths:
+{{ range $i, $path := .paths }}
+ - {{$path}}
+{{ end }}
diff --git a/filebeat/tests/system/module/test/test/ingest/pipeline.json b/filebeat/tests/system/module/test/test/ingest/pipeline.json
new file mode 100644
index 000000000000..0967ef424bce
--- /dev/null
+++ b/filebeat/tests/system/module/test/test/ingest/pipeline.json
@@ -0,0 +1 @@
+{}
diff --git a/filebeat/tests/system/module/test/test/manifest.yml b/filebeat/tests/system/module/test/test/manifest.yml
new file mode 100644
index 000000000000..8b90842943f1
--- /dev/null
+++ b/filebeat/tests/system/module/test/test/manifest.yml
@@ -0,0 +1,9 @@
+module_version: "1.0"
+
+var:
+  - name: paths
+    default:
+      - test.log
+
+ingest_pipeline: ingest/pipeline.json
+prospector: config/test.yml
diff --git a/filebeat/tests/system/test_reload_modules.py b/filebeat/tests/system/test_reload_modules.py
new file mode 100644
index 000000000000..d6b3f183ff52
--- /dev/null
+++ b/filebeat/tests/system/test_reload_modules.py
@@ -0,0 +1,152 @@
+import re
+import sys
+import unittest
+import os
+import shutil
+import time
+from filebeat import BaseTest
+
+
+moduleConfigTemplate = """
+- module: test
+  test:
+    enabled: true
+    var.paths:
+      - {}
+    prospector:
+      scan_frequency: 1s
+  auth:
+    enabled: false
+"""
+
+
+class Test(BaseTest):
+
+    def setUp(self):
+        super(BaseTest, self).setUp()
+        # Copy system module
+        shutil.copytree(os.path.join("module", "test"),
+                        os.path.join(self.working_dir, "module", "test"))
+
+    def test_reload(self):
+        """
+        Test modules basic reload
+        """
+        self.render_config_template(
+            reload=True,
+            reload_path=self.working_dir + "/configs/*.yml",
+            reload_type="modules",
+            prospectors=False,
+        )
+
+        proc = self.start_beat()
+
+        os.mkdir(self.working_dir + "/logs/")
+        logfile = self.working_dir + "/logs/test.log"
+        os.mkdir(self.working_dir + "/configs/")
+
+        with open(self.working_dir + "/configs/system.yml.test", 'w') as f:
+            f.write(moduleConfigTemplate.format(self.working_dir + "/logs/*"))
+        os.rename(self.working_dir + "/configs/system.yml.test",
+                  self.working_dir + "/configs/system.yml")
+
+        with open(logfile, 'w') as f:
+            f.write("Hello world\n")
+
+        self.wait_until(lambda: self.output_lines() > 0)
+        assert self.output_has_message("Hello world")
+        proc.check_kill_and_wait()
+
+    def test_start_stop(self):
+        """
+        Test basic modules start and stop
+        """
+        self.render_config_template(
+            reload=True,
+            reload_path=self.working_dir + "/configs/*.yml",
+            reload_type="modules",
+            prospectors=False,
+        )
+
+        proc = self.start_beat()
+
+        os.mkdir(self.working_dir + "/logs/")
+        logfile = self.working_dir + "/logs/test.log"
+        os.mkdir(self.working_dir + "/configs/")
+
+        with open(self.working_dir + "/configs/system.yml.test", 'w') as f:
+            f.write(moduleConfigTemplate.format(self.working_dir + "/logs/*"))
+        os.rename(self.working_dir + "/configs/system.yml.test",
+                  self.working_dir + "/configs/system.yml")
+
+        with open(logfile, 'w') as f:
+            f.write("Hello world\n")
+
+        self.wait_until(lambda: self.output_lines() == 1, max_timeout=10)
+        print(self.output_lines())
+
+        # Remove prospector
+        with open(self.working_dir + "/configs/system.yml", 'w') as f:
+            f.write("")
+
+        # Wait until prospector is stopped
+        self.wait_until(
+            lambda: self.log_contains("Runner stopped:"),
+            max_timeout=15)
+
+        with open(logfile, 'a') as f:
+            f.write("Hello world\n")
+
+        # Wait to give a change to pick up the new line (it shouldn't)
+        time.sleep(1)
+
+        self.wait_until(lambda: self.output_lines() == 1, max_timeout=5)
+        proc.check_kill_and_wait()
+
+    def test_load_configs(self):
+        """
+        Test loading separate module configs
+        """
+        self.render_config_template(
+            reload_path=self.working_dir + "/configs/*.yml",
+            reload_type="modules",
+            prospectors=False,
+        )
+
+        os.mkdir(self.working_dir + "/logs/")
+        os.mkdir(self.working_dir + "/configs/")
+        logfile1 = self.working_dir + "/logs/test1.log"
+        logfile2 = self.working_dir + "/logs/test2.log"
+
+        with open(self.working_dir + "/configs/module1.yml", 'w') as f:
+            f.write(moduleConfigTemplate.format(
+                self.working_dir + "/logs/test1.log"))
+
+        with open(self.working_dir + "/configs/module2.yml", 'w') as f:
+            f.write(moduleConfigTemplate.format(
+                self.working_dir + "/logs/test2.log"))
+
+        proc = self.start_beat()
+
+        with open(logfile1, 'w') as f:
+            f.write("Hello 1\n")
+
+        self.wait_until(lambda: self.output_lines() == 1)
+
+        with open(logfile2, 'w') as f:
+            f.write("Hello 2\n")
+
+        self.wait_until(lambda: self.output_lines() == 2)
+
+        output = self.read_output()
+
+        # Reloading stopped.
+        self.wait_until(
+            lambda: self.log_contains("Loading of config files completed."),
+            max_timeout=15)
+
+        # Make sure the correct lines were picked up
+        assert self.output_lines() == 2
+        assert output[0]["message"] == "Hello 1"
+        assert output[1]["message"] == "Hello 2"
+        proc.check_kill_and_wait()
diff --git a/filebeat/tests/system/test_reload.py b/filebeat/tests/system/test_reload_prospectors.py
similarity index 98%
rename from filebeat/tests/system/test_reload.py
rename to filebeat/tests/system/test_reload_prospectors.py
index 084d2a01eab5..d9db94c8c50f 100644
--- a/filebeat/tests/system/test_reload.py
+++ b/filebeat/tests/system/test_reload_prospectors.py
@@ -18,7 +18,7 @@ class Test(BaseTest):
 
     def test_reload(self):
         """
-        Test basic reload
+        Test basic prospectors reload
         """
         self.render_config_template(
             reload=True,
@@ -43,7 +43,7 @@ def test_reload(self):
 
     def test_start_stop(self):
         """
-        Test basic start and stop
+        Test basic prospectors start and stop
         """
         self.render_config_template(
             reload=True,
@@ -86,7 +86,7 @@ def test_start_stop(self):
 
     def test_start_stop_replace(self):
         """
-        Test basic start and replace with an other prospecto
+        Test basic start and replace with another prospector
         """
         self.render_config_template(
             reload=True,