diff --git a/x-pack/elastic-agent/_meta/config/common.reference.p2.yml.tmpl b/x-pack/elastic-agent/_meta/config/common.reference.p2.yml.tmpl
index bfb84102e3c..5daf9d81432 100644
--- a/x-pack/elastic-agent/_meta/config/common.reference.p2.yml.tmpl
+++ b/x-pack/elastic-agent/_meta/config/common.reference.p2.yml.tmpl
@@ -121,7 +121,7 @@ inputs:
 #       port: 6791
 
 # # Allow fleet to reload its configuration locally on disk.
-# # Notes: Only specific process configuration will be reloaded.
+# # Notes: Only specific process configuration and external input configurations will be reloaded.
 # agent.reload:
 #   # enabled configure the Elastic Agent to reload or not the local configuration.
 #   #
diff --git a/x-pack/elastic-agent/elastic-agent.reference.yml b/x-pack/elastic-agent/elastic-agent.reference.yml
index 7770b036dba..7b2d5ea586c 100644
--- a/x-pack/elastic-agent/elastic-agent.reference.yml
+++ b/x-pack/elastic-agent/elastic-agent.reference.yml
@@ -127,7 +127,7 @@ inputs:
 #       port: 6791
 
 # # Allow fleet to reload its configuration locally on disk.
-# # Notes: Only specific process configuration will be reloaded.
+# # Notes: Only specific process configuration and external input configurations will be reloaded.
 # agent.reload:
 #   # enabled configure the Elastic Agent to reload or not the local configuration.
 #   #
diff --git a/x-pack/elastic-agent/pkg/agent/application/fleet_server_bootstrap.go b/x-pack/elastic-agent/pkg/agent/application/fleet_server_bootstrap.go
index 89cb816fec9..76ff369ef6a 100644
--- a/x-pack/elastic-agent/pkg/agent/application/fleet_server_bootstrap.go
+++ b/x-pack/elastic-agent/pkg/agent/application/fleet_server_bootstrap.go
@@ -118,8 +118,9 @@ func newFleetServerBootstrap(
 		return nil, err
 	}
 
+	loader := config.NewLoader(log, "")
 	discover := discoverer(pathConfigFile, cfg.Settings.Path)
-	bootstrapApp.source = newOnce(log, discover, emit)
+	bootstrapApp.source = newOnce(log, discover, loader, emit)
 	return bootstrapApp, nil
 }
 
diff --git a/x-pack/elastic-agent/pkg/agent/application/local_mode.go b/x-pack/elastic-agent/pkg/agent/application/local_mode.go
index a29977f2e8d..ca8284cdf8e 100644
--- a/x-pack/elastic-agent/pkg/agent/application/local_mode.go
+++ b/x-pack/elastic-agent/pkg/agent/application/local_mode.go
@@ -6,6 +6,7 @@ package application
 
 import (
 	"context"
+	"path/filepath"
 
 	"go.elastic.co/apm"
 
@@ -117,7 +118,7 @@ func newLocal(
 		return nil, errors.New(err, "failed to initialize composable controller")
 	}
 
-	discover := discoverer(pathConfigFile, cfg.Settings.Path)
+	discover := discoverer(pathConfigFile, cfg.Settings.Path, configuration.ExternalInputsPattern)
 	emit, err := emitter.New(
 		localApplication.bgContext,
 		log,
@@ -135,13 +136,15 @@ func newLocal(
 		return nil, err
 	}
 
+	loader := config.NewLoader(log, externalConfigsGlob())
+
 	var cfgSource source
 	if !cfg.Settings.Reload.Enabled {
 		log.Debug("Reloading of configuration is off")
-		cfgSource = newOnce(log, discover, emit)
+		cfgSource = newOnce(log, discover, loader, emit)
 	} else {
 		log.Debugf("Reloading of configuration is on, frequency is set to %s", cfg.Settings.Reload.Period)
-		cfgSource = newPeriodic(log, cfg.Settings.Reload.Period, discover, emit)
+		cfgSource = newPeriodic(log, cfg.Settings.Reload.Period, discover, loader, emit)
 	}
 
 	localApplication.source = cfgSource
@@ -161,6 +164,10 @@ func newLocal(
 	return localApplication, nil
 }
 
+func externalConfigsGlob() string {
+	return filepath.Join(paths.Config(), configuration.ExternalInputsPattern)
+}
+
 // Routes returns a list of routes handled by agent.
 func (l *Local) Routes() *sorted.Set {
 	return l.router.Routes()
diff --git a/x-pack/elastic-agent/pkg/agent/application/once.go b/x-pack/elastic-agent/pkg/agent/application/once.go
index 64ee34e2590..db4af015608 100644
--- a/x-pack/elastic-agent/pkg/agent/application/once.go
+++ b/x-pack/elastic-agent/pkg/agent/application/once.go
@@ -16,11 +16,12 @@ import (
 type once struct {
 	log      *logger.Logger
 	discover discoverFunc
+	loader   *config.Loader
 	emitter  pipeline.EmitterFunc
 }
 
-func newOnce(log *logger.Logger, discover discoverFunc, emitter pipeline.EmitterFunc) *once {
-	return &once{log: log, discover: discover, emitter: emitter}
+func newOnce(log *logger.Logger, discover discoverFunc, loader *config.Loader, emitter pipeline.EmitterFunc) *once {
+	return &once{log: log, discover: discover, loader: loader, emitter: emitter}
 }
 
 func (o *once) Start() error {
@@ -33,15 +34,15 @@ func (o *once) Start() error {
 		return ErrNoConfiguration
 	}
 
-	return readfiles(context.Background(), files, o.emitter)
+	return readfiles(context.Background(), files, o.loader, o.emitter)
 }
 
 func (o *once) Stop() error {
 	return nil
 }
 
-func readfiles(ctx context.Context, files []string, emitter pipeline.EmitterFunc) error {
-	c, err := config.LoadFiles(files...)
+func readfiles(ctx context.Context, files []string, loader *config.Loader, emitter pipeline.EmitterFunc) error {
+	c, err := loader.Load(files)
 	if err != nil {
 		return errors.New(err, "could not load or merge configuration", errors.TypeConfig)
 	}
diff --git a/x-pack/elastic-agent/pkg/agent/application/periodic.go b/x-pack/elastic-agent/pkg/agent/application/periodic.go
index f79c09b6e68..119e616bf28 100644
--- a/x-pack/elastic-agent/pkg/agent/application/periodic.go
+++ b/x-pack/elastic-agent/pkg/agent/application/periodic.go
@@ -11,6 +11,7 @@ import (
 
 	"github.com/elastic/beats/v7/x-pack/elastic-agent/pkg/agent/application/pipeline"
 	"github.com/elastic/beats/v7/x-pack/elastic-agent/pkg/agent/errors"
+	"github.com/elastic/beats/v7/x-pack/elastic-agent/pkg/config"
 	"github.com/elastic/beats/v7/x-pack/elastic-agent/pkg/core/logger"
 	"github.com/elastic/beats/v7/x-pack/elastic-agent/pkg/filewatcher"
 )
@@ -20,6 +21,7 @@ type periodic struct {
 	period   time.Duration
 	done     chan struct{}
 	watcher  *filewatcher.Watch
+	loader   *config.Loader
 	emitter  pipeline.EmitterFunc
 	discover discoverFunc
 }
@@ -90,7 +92,7 @@ func (p *periodic) work() error {
 			p.log.Debugf("Unchanged %d files: %s", len(s.Unchanged), strings.Join(s.Updated, ", "))
 		}
 
-		err := readfiles(context.Background(), files, p.emitter)
+		err := readfiles(context.Background(), files, p.loader, p.emitter)
 		if err != nil {
 			// assume something when really wrong and invalidate any cache
 			// so we get a full new config on next tick.
@@ -112,6 +114,7 @@ func newPeriodic(
 	log *logger.Logger,
 	period time.Duration,
 	discover discoverFunc,
+	loader *config.Loader,
 	emitter pipeline.EmitterFunc,
 ) *periodic {
 	w, err := filewatcher.New(log, filewatcher.DefaultComparer)
@@ -127,6 +130,7 @@ func newPeriodic(
 		done:     make(chan struct{}),
 		watcher:  w,
 		discover: discover,
+		loader:   loader,
 		emitter:  emitter,
 	}
 }
diff --git a/x-pack/elastic-agent/pkg/agent/configuration/settings.go b/x-pack/elastic-agent/pkg/agent/configuration/settings.go
index 3081614d995..4f2a17dbede 100644
--- a/x-pack/elastic-agent/pkg/agent/configuration/settings.go
+++ b/x-pack/elastic-agent/pkg/agent/configuration/settings.go
@@ -5,6 +5,8 @@
 package configuration
 
 import (
+	"path/filepath"
+
 	"github.com/elastic/beats/v7/x-pack/elastic-agent/pkg/artifact"
 	"github.com/elastic/beats/v7/x-pack/elastic-agent/pkg/core/logger"
 	monitoringCfg "github.com/elastic/beats/v7/x-pack/elastic-agent/pkg/core/monitoring/config"
@@ -13,6 +15,9 @@ import (
 	"github.com/elastic/beats/v7/x-pack/elastic-agent/pkg/core/server"
 )
 
+// ExternalInputsPattern is a glob that matches the paths of external configuration files.
+var ExternalInputsPattern = filepath.Join("inputs.d", "*.yml")
+
 // SettingsConfig is an collection of agent settings configuration.
 type SettingsConfig struct {
 	DownloadConfig   *artifact.Config                `yaml:"download" config:"download" json:"download"`
diff --git a/x-pack/elastic-agent/pkg/config/loader.go b/x-pack/elastic-agent/pkg/config/loader.go
new file mode 100644
index 00000000000..8827edd6c3c
--- /dev/null
+++ b/x-pack/elastic-agent/pkg/config/loader.go
@@ -0,0 +1,104 @@
+// Copyright Elasticsearch B.V. and/or licensed to Elasticsearch B.V. under one
+// or more contributor license agreements. Licensed under the Elastic License;
+// you may not use this file except in compliance with the Elastic License.
+
+package config
+
+import (
+	"fmt"
+	"path/filepath"
+
+	"github.com/elastic/beats/v7/x-pack/elastic-agent/pkg/core/logger"
+	"github.com/elastic/go-ucfg"
+	"github.com/elastic/go-ucfg/cfgutil"
+)
+
+// Loader is used to load configuration from the paths
+// including appending multiple input configurations.
+type Loader struct {
+	logger       *logger.Logger
+	inputsFolder string
+}
+
+// NewLoader creates a new Loader instance to load configuration
+// files from different paths.
+func NewLoader(logger *logger.Logger, inputsFolder string) *Loader {
+	return &Loader{logger: logger, inputsFolder: inputsFolder}
+}
+
+// Load iterates over the list of files and loads the confguration from them.
+// If a configuration file is under the folder set in `agent.config.inputs.path`
+// it is appended to a list. If it is a regular config file, it is merged into
+// the result config. The list of input configurations is merged into the result
+// last.
+func (l *Loader) Load(files []string) (*Config, error) {
+	inputsList := make([]*ucfg.Config, 0)
+	merger := cfgutil.NewCollector(nil)
+	for _, f := range files {
+		cfg, err := LoadFile(f)
+		if err != nil {
+			if l.isFileUnderInputsFolder(f) {
+				return nil, fmt.Errorf("failed to load external configuration file '%s': %w. Are you sure it contains an inputs section?", f, err)
+			}
+			return nil, fmt.Errorf("failed to load configuration file '%s': %w", f, err)
+		}
+		l.logger.Debugf("Loaded configuration from %s", f)
+		if l.isFileUnderInputsFolder(f) {
+			inp, err := getInput(cfg)
+			if err != nil {
+				return nil, fmt.Errorf("cannot get configuration from '%s': %w", f, err)
+			}
+			inputsList = append(inputsList, inp...)
+			l.logger.Debugf("Loaded %s input(s) from configuration from %s", len(inp), f)
+		} else {
+			if err := merger.Add(cfg.access(), err); err != nil {
+				return nil, fmt.Errorf("failed to merge configuration file '%s' to existing one: %w", f, err)
+			}
+			l.logger.Debugf("Merged configuration from %s into result", f)
+		}
+	}
+	config := merger.Config()
+
+	// if there is no input configuration, return what we have collected.
+	if len(inputsList) == 0 {
+		l.logger.Debugf("Merged all configuration files from %v, no external input files", files)
+		return newConfigFrom(config), nil
+	}
+
+	// merge inputs sections from the last standalone configuration
+	// file and all files from the inputs folder
+	start := 0
+	if config.HasField("inputs") {
+		var err error
+		start, err = config.CountField("inputs")
+		if err != nil {
+			return nil, fmt.Errorf("failed to count the number of inputs in the configuration: %w", err)
+		}
+	}
+	for i, ll := range inputsList {
+		if err := config.SetChild("inputs", start+i, ll); err != nil {
+			return nil, fmt.Errorf("failed to add inputs to result configuration: %w", err)
+		}
+	}
+
+	l.logger.Debugf("Merged all configuration files from %v, with external input files", files)
+	return newConfigFrom(config), nil
+}
+
+func getInput(c *Config) ([]*ucfg.Config, error) {
+	tmpConfig := struct {
+		Inputs []*ucfg.Config `config:"inputs"`
+	}{make([]*ucfg.Config, 0)}
+
+	if err := c.Unpack(&tmpConfig); err != nil {
+		return nil, fmt.Errorf("failed to parse inputs section from configuration: %w", err)
+	}
+	return tmpConfig.Inputs, nil
+}
+
+func (l *Loader) isFileUnderInputsFolder(f string) bool {
+	if matches, err := filepath.Match(l.inputsFolder, f); !matches || err != nil {
+		return false
+	}
+	return true
+}
diff --git a/x-pack/elastic-agent/pkg/config/loader_test.go b/x-pack/elastic-agent/pkg/config/loader_test.go
new file mode 100644
index 00000000000..d1766622663
--- /dev/null
+++ b/x-pack/elastic-agent/pkg/config/loader_test.go
@@ -0,0 +1,212 @@
+// Copyright Elasticsearch B.V. and/or licensed to Elasticsearch B.V. under one
+// or more contributor license agreements. Licensed under the Elastic License;
+// you may not use this file except in compliance with the Elastic License.
+
+package config
+
+import (
+	"path/filepath"
+	"testing"
+
+	"github.com/stretchr/testify/require"
+
+	"github.com/elastic/beats/v7/x-pack/elastic-agent/pkg/core/logger"
+)
+
+func TestExternalConfigLoading(t *testing.T) {
+	cases := map[string]struct {
+		configs        []string
+		inputsFolder   string
+		expectedConfig map[string]interface{}
+		err            bool
+	}{
+		"non-existent config files lead to error": {
+			configs: []string{"no-such-configuration-file.yml"},
+			err:     true,
+		},
+		"invalid configuration file in inputs folder lead to error": {
+			configs: []string{
+				filepath.Join("testdata", "inputs", "invalid-inputs.yml"),
+			},
+			inputsFolder: filepath.Join("testdata", "inputs", "*.yml"),
+			err:          true,
+		},
+		"two standalone configs can be merged without inputs": {
+			configs: []string{
+				filepath.Join("testdata", "standalone1.yml"),
+				filepath.Join("testdata", "standalone2.yml"),
+			},
+			inputsFolder: "",
+			expectedConfig: map[string]interface{}{
+				"outputs": map[string]interface{}{
+					"default": map[string]interface{}{
+						"type":    "elasticsearch",
+						"hosts":   []interface{}{"127.0.0.1:9201"},
+						"api-key": "my-secret-key",
+					},
+				},
+				"agent": map[string]interface{}{
+					"logging": map[string]interface{}{
+						"level": "debug",
+						"metrics": map[string]interface{}{
+							"enabled": false,
+						},
+					},
+				},
+			},
+		},
+		"one external config, standalone config without inputs section": {
+			configs: []string{
+				filepath.Join("testdata", "standalone1.yml"),
+				filepath.Join("testdata", "inputs", "log-inputs.yml"),
+				filepath.Join("testdata", "inputs", "metrics-inputs.yml"),
+			},
+			inputsFolder: filepath.Join("testdata", "inputs", "*.yml"),
+			expectedConfig: map[string]interface{}{
+				"outputs": map[string]interface{}{
+					"default": map[string]interface{}{
+						"type":    "elasticsearch",
+						"hosts":   []interface{}{"127.0.0.1:9201"},
+						"api-key": "my-secret-key",
+					},
+				},
+				"inputs": []interface{}{
+					map[string]interface{}{
+						"data_stream": map[string]interface{}{
+							"dataset": "system.auth",
+							"type":    "logs",
+						},
+						"exclude_files": []interface{}{".gz$"},
+						"id":            "logfile-system.auth-my-id",
+						"paths":         []interface{}{"/var/log/auth.log*", "/var/log/secure*"},
+						"use_output":    "default",
+					},
+					map[string]interface{}{
+						"data_stream": map[string]interface{}{
+							"dataset": "system.syslog",
+							"type":    "logs",
+						},
+						"type":          "logfile",
+						"id":            "logfile-system.syslog-my-id",
+						"exclude_files": []interface{}{".gz$"},
+						"paths":         []interface{}{"/var/log/messages*", "/var/log/syslog*"},
+						"use_output":    "default",
+					},
+					map[string]interface{}{
+						"data_stream": map[string]interface{}{
+							"dataset": "system.diskio",
+							"type":    "metrics",
+						},
+						"id":         "system/metrics-system.diskio-my-id",
+						"metricsets": []interface{}{"diskio"},
+						"period":     "10s",
+					},
+					map[string]interface{}{
+						"data_stream": map[string]interface{}{
+							"dataset": "system.filesystem",
+							"type":    "metrics",
+						},
+						"id":         "system/metrics-system.filesystem-my-id",
+						"metricsets": []interface{}{"filesystem"},
+						"period":     "30s",
+					},
+				},
+			},
+		},
+		"inputs sections of all external and standalone configuration are merged to the result": {
+			configs: []string{
+				filepath.Join("testdata", "standalone-with-inputs.yml"),
+				filepath.Join("testdata", "inputs", "log-inputs.yml"),
+				filepath.Join("testdata", "inputs", "metrics-inputs.yml"),
+			},
+			inputsFolder: filepath.Join("testdata", "inputs", "*.yml"),
+			expectedConfig: map[string]interface{}{
+				"outputs": map[string]interface{}{
+					"default": map[string]interface{}{
+						"type":    "elasticsearch",
+						"hosts":   []interface{}{"127.0.0.1:9201"},
+						"api-key": "my-secret-key",
+					},
+				},
+				"inputs": []interface{}{
+					map[string]interface{}{
+						"type":                  "system/metrics",
+						"data_stream.namespace": "default",
+						"use_output":            "default",
+						"streams": []interface{}{
+							map[string]interface{}{
+								"metricset":           "cpu",
+								"data_stream.dataset": "system.cpu",
+							},
+						},
+					},
+					map[string]interface{}{
+						"data_stream": map[string]interface{}{
+							"dataset": "system.auth",
+							"type":    "logs",
+						},
+						"exclude_files": []interface{}{".gz$"},
+						"id":            "logfile-system.auth-my-id",
+						"paths":         []interface{}{"/var/log/auth.log*", "/var/log/secure*"},
+						"use_output":    "default",
+					},
+					map[string]interface{}{
+						"data_stream": map[string]interface{}{
+							"dataset": "system.syslog",
+							"type":    "logs",
+						},
+						"type":          "logfile",
+						"id":            "logfile-system.syslog-my-id",
+						"exclude_files": []interface{}{".gz$"},
+						"paths":         []interface{}{"/var/log/messages*", "/var/log/syslog*"},
+						"use_output":    "default",
+					},
+					map[string]interface{}{
+						"data_stream": map[string]interface{}{
+							"dataset": "system.diskio",
+							"type":    "metrics",
+						},
+						"id":         "system/metrics-system.diskio-my-id",
+						"metricsets": []interface{}{"diskio"},
+						"period":     "10s",
+					},
+					map[string]interface{}{
+						"data_stream": map[string]interface{}{
+							"dataset": "system.filesystem",
+							"type":    "metrics",
+						},
+						"id":         "system/metrics-system.filesystem-my-id",
+						"metricsets": []interface{}{"filesystem"},
+						"period":     "30s",
+					},
+				},
+			},
+		},
+	}
+
+	for name, test := range cases {
+		t.Run(name, func(t *testing.T) {
+			test := test
+
+			l := mustNewLoader(test.inputsFolder)
+			c, err := l.Load(test.configs)
+			if test.err {
+				require.NotNil(t, err)
+				return
+			}
+
+			require.Nil(t, err)
+			raw, err := c.ToMapStr()
+			require.Nil(t, err)
+			require.Equal(t, test.expectedConfig, raw)
+		})
+	}
+}
+
+func mustNewLoader(inputsFolder string) *Loader {
+	log, err := logger.New("loader_test", true)
+	if err != nil {
+		panic(err)
+	}
+	return NewLoader(log, inputsFolder)
+}
diff --git a/x-pack/elastic-agent/pkg/config/testdata/inputs/invalid-inputs.yml b/x-pack/elastic-agent/pkg/config/testdata/inputs/invalid-inputs.yml
new file mode 100644
index 00000000000..b6da68a339e
--- /dev/null
+++ b/x-pack/elastic-agent/pkg/config/testdata/inputs/invalid-inputs.yml
@@ -0,0 +1,5 @@
+# this file is invalid because the inputs section is missing
+- data_stream:
+    dataset: system.auth
+    type: logs
+
diff --git a/x-pack/elastic-agent/pkg/config/testdata/inputs/log-inputs.yml b/x-pack/elastic-agent/pkg/config/testdata/inputs/log-inputs.yml
new file mode 100644
index 00000000000..cead269b0a3
--- /dev/null
+++ b/x-pack/elastic-agent/pkg/config/testdata/inputs/log-inputs.yml
@@ -0,0 +1,20 @@
+inputs:
+- data_stream:
+    dataset: system.auth
+    type: logs
+  exclude_files: [".gz$"]
+  id: logfile-system.auth-my-id
+  paths:
+  - /var/log/auth.log*
+  - /var/log/secure*
+  use_output: default
+- data_stream:
+    dataset: system.syslog
+    type: logs
+  type: logfile
+  id: logfile-system.syslog-my-id
+  exclude_files: [".gz$"]
+  paths:
+  - /var/log/messages*
+  - /var/log/syslog*
+  use_output: default
diff --git a/x-pack/elastic-agent/pkg/config/testdata/inputs/metrics-inputs.yml b/x-pack/elastic-agent/pkg/config/testdata/inputs/metrics-inputs.yml
new file mode 100644
index 00000000000..b44faf5097d
--- /dev/null
+++ b/x-pack/elastic-agent/pkg/config/testdata/inputs/metrics-inputs.yml
@@ -0,0 +1,16 @@
+inputs:
+- data_stream:
+    dataset: system.diskio
+    type: metrics
+  id: system/metrics-system.diskio-my-id
+  metricsets:
+  - diskio
+  period: 10s
+- data_stream:
+    dataset: system.filesystem
+    type: metrics
+  id: system/metrics-system.filesystem-my-id
+  metricsets:
+  - filesystem
+  period: 30s
+
diff --git a/x-pack/elastic-agent/pkg/config/testdata/standalone-with-inputs.yml b/x-pack/elastic-agent/pkg/config/testdata/standalone-with-inputs.yml
new file mode 100644
index 00000000000..1be5ac9daec
--- /dev/null
+++ b/x-pack/elastic-agent/pkg/config/testdata/standalone-with-inputs.yml
@@ -0,0 +1,13 @@
+outputs:
+  default:
+    type: elasticsearch
+    hosts: [127.0.0.1:9201]
+    api-key: "my-secret-key"
+
+inputs:
+  - type: system/metrics
+    data_stream.namespace: default
+    use_output: default
+    streams:
+      - metricset: cpu
+        data_stream.dataset: system.cpu
diff --git a/x-pack/elastic-agent/pkg/config/testdata/standalone1.yml b/x-pack/elastic-agent/pkg/config/testdata/standalone1.yml
new file mode 100644
index 00000000000..f0ddddf1a2a
--- /dev/null
+++ b/x-pack/elastic-agent/pkg/config/testdata/standalone1.yml
@@ -0,0 +1,6 @@
+outputs:
+  default:
+    type: elasticsearch
+    hosts: [127.0.0.1:9201]
+    api-key: "my-secret-key"
+
diff --git a/x-pack/elastic-agent/pkg/config/testdata/standalone2.yml b/x-pack/elastic-agent/pkg/config/testdata/standalone2.yml
new file mode 100644
index 00000000000..7183b32b79f
--- /dev/null
+++ b/x-pack/elastic-agent/pkg/config/testdata/standalone2.yml
@@ -0,0 +1,3 @@
+agent.logging.level: debug
+agent.logging.metrics.enabled: false
+