diff --git a/CHANGELOG.next.asciidoc b/CHANGELOG.next.asciidoc
index 8600f545e6f..77355006d6e 100644
--- a/CHANGELOG.next.asciidoc
+++ b/CHANGELOG.next.asciidoc
@@ -32,6 +32,7 @@ https://github.com/elastic/beats/compare/v7.0.0-alpha2...master[Check the HEAD d
 - Rename a few `logstash.*` fields to map to ECS, remove logstash.slowlog.message. {pull}9935[9935]
 - Rename a few `mysql.*` fields to map to ECS. {pull}10008[10008]
 - Rename a few `nginx.error.*` fields to map to ECS. {pull}10007[10007]
+- Filesets with multiple ingest pipelines added in {pull}8914[8914] only work with Elasticsearch >= 6.5.0 {pull}10001[10001]
 
 *Heartbeat*
 
diff --git a/filebeat/fileset/pipelines.go b/filebeat/fileset/pipelines.go
index 0b6e853ce22..07e520d64f8 100644
--- a/filebeat/fileset/pipelines.go
+++ b/filebeat/fileset/pipelines.go
@@ -39,6 +39,25 @@ type PipelineLoader interface {
 	GetVersion() common.Version
 }
 
+// MultiplePipelineUnsupportedError is an error returned when a fileset uses multiple pipelines but is
+// running against a version of Elasticsearch that doesn't support this feature.
+type MultiplePipelineUnsupportedError struct {
+	module               string
+	fileset              string
+	esVersion            common.Version
+	minESVersionRequired common.Version
+}
+
+func (m MultiplePipelineUnsupportedError) Error() string {
+	return fmt.Sprintf(
+		"the %s/%s fileset has multiple pipelines, which are only supported with Elasticsearch >= %s. Currently running with Elasticsearch version %s",
+		m.module,
+		m.fileset,
+		m.minESVersionRequired.String(),
+		m.esVersion.String(),
+	)
+}
+
 // LoadPipelines loads the pipelines for each configured fileset.
 func (reg *ModuleRegistry) LoadPipelines(esClient PipelineLoader, overwrite bool) error {
 	for module, filesets := range reg.registry {
@@ -58,6 +77,13 @@ func (reg *ModuleRegistry) LoadPipelines(esClient PipelineLoader, overwrite bool
 				return fmt.Errorf("Error getting pipeline for fileset %s/%s: %v", module, name, err)
 			}
 
+			// Filesets with multiple pipelines can only be supported by Elasticsearch >= 6.5.0
+			esVersion := esClient.GetVersion()
+			minESVersionRequired := common.MustNewVersion("6.5.0")
+			if len(pipelines) > 1 && esVersion.LessThan(minESVersionRequired) {
+				return MultiplePipelineUnsupportedError{module, name, esVersion, *minESVersionRequired}
+			}
+
 			var pipelineIDsLoaded []string
 			for _, pipeline := range pipelines {
 				err = loadPipeline(esClient, pipeline.id, pipeline.contents, overwrite)
diff --git a/filebeat/fileset/pipelines_test.go b/filebeat/fileset/pipelines_test.go
new file mode 100644
index 00000000000..194df5e9f14
--- /dev/null
+++ b/filebeat/fileset/pipelines_test.go
@@ -0,0 +1,105 @@
+// Licensed to Elasticsearch B.V. under one or more contributor
+// license agreements. See the NOTICE file distributed with
+// this work for additional information regarding copyright
+// ownership. Elasticsearch B.V. licenses this file to you under
+// the Apache License, Version 2.0 (the "License"); you may
+// not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing,
+// software distributed under the License is distributed on an
+// "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+// KIND, either express or implied.  See the License for the
+// specific language governing permissions and limitations
+// under the License.
+
+// +build !integration
+
+package fileset
+
+import (
+	"net/http"
+	"net/http/httptest"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+
+	"github.com/elastic/beats/libbeat/outputs/elasticsearch"
+)
+
+func TestLoadPipelinesWithMultiPipelineFileset(t *testing.T) {
+	cases := []struct {
+		name          string
+		esVersion     string
+		isErrExpected bool
+	}{
+		{
+			name:          "ES < 6.5.0",
+			esVersion:     "6.4.1",
+			isErrExpected: true,
+		},
+		{
+			name:          "ES == 6.5.0",
+			esVersion:     "6.5.0",
+			isErrExpected: false,
+		},
+		{
+			name:          "ES > 6.5.0",
+			esVersion:     "6.6.0",
+			isErrExpected: false,
+		},
+	}
+
+	for _, test := range cases {
+		test := test
+		t.Run(test.name, func(t *testing.T) {
+			t.Parallel()
+			testFilesetManifest := &manifest{
+				Requires: struct {
+					Processors []ProcessorRequirement `config:"processors"`
+				}{
+					Processors: []ProcessorRequirement{},
+				},
+				IngestPipeline: []string{"pipeline-plain.json", "pipeline-json.json"},
+			}
+			testFileset := &Fileset{
+				name:       "fls",
+				modulePath: "./test/mod",
+				manifest:   testFilesetManifest,
+				vars: map[string]interface{}{
+					"builtin": map[string]interface{}{},
+				},
+				pipelineIDs: []string{"filebeat-7.0.0-mod-fls-pipeline-plain", "filebeat-7.0.0-mod-fls-pipeline-json"},
+			}
+			testRegistry := ModuleRegistry{
+				registry: map[string]map[string]*Fileset{
+					"mod": map[string]*Fileset{
+						"fls": testFileset,
+					},
+				},
+			}
+
+			testESServer := httptest.NewServer(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+				w.Write([]byte("{\"version\":{\"number\":\"" + test.esVersion + "\"}}"))
+			}))
+			defer testESServer.Close()
+
+			testESClient, err := elasticsearch.NewClient(elasticsearch.ClientSettings{
+				URL: testESServer.URL,
+			}, nil)
+			assert.NoError(t, err)
+
+			err = testESClient.Connect()
+			assert.NoError(t, err)
+
+			err = testRegistry.LoadPipelines(testESClient, false)
+			if test.isErrExpected {
+				assert.IsType(t, MultiplePipelineUnsupportedError{}, err)
+			} else {
+				assert.NoError(t, err)
+			}
+		})
+	}
+}
diff --git a/filebeat/fileset/test/mod/fls/pipeline-json.json b/filebeat/fileset/test/mod/fls/pipeline-json.json
new file mode 100644
index 00000000000..0967ef424bc
--- /dev/null
+++ b/filebeat/fileset/test/mod/fls/pipeline-json.json
@@ -0,0 +1 @@
+{}
diff --git a/filebeat/fileset/test/mod/fls/pipeline-plain.json b/filebeat/fileset/test/mod/fls/pipeline-plain.json
new file mode 100644
index 00000000000..0967ef424bc
--- /dev/null
+++ b/filebeat/fileset/test/mod/fls/pipeline-plain.json
@@ -0,0 +1 @@
+{}
diff --git a/filebeat/fileset/test/pipeline-plain.json b/filebeat/fileset/test/pipeline-plain.json
new file mode 100644
index 00000000000..e69de29bb2d