diff --git a/CHANGELOG.next.asciidoc b/CHANGELOG.next.asciidoc
index e85dcb6a479f..a4f0aac6954c 100644
--- a/CHANGELOG.next.asciidoc
+++ b/CHANGELOG.next.asciidoc
@@ -64,6 +64,7 @@ https://github.com/elastic/beats/compare/v7.0.0-alpha2...master[Check the HEAD d
 - Not hiding error in case of http failure using elastic fetcher {pull}11604[11604]
 - Relax validation of the X-Pack license UID value. {issue}11640[11640]
 - Fix a parsing error with the X-Pack license check on 32-bit system. {issue}11650[11650]
+- Escape BOM on JsonReader before trying to decode line {pull}11661[11661]
 - Fix ILM policy always being overwritten. {pull}11671[11671]
 - Fix template always being overwritten. {pull}11671[11671]
 - Fix matching of string arrays in contains condition. {pull}11691[11691]
diff --git a/filebeat/input/log/harvester.go b/filebeat/input/log/harvester.go
index 23cf62d26e43..469ae109da9d 100644
--- a/filebeat/input/log/harvester.go
+++ b/filebeat/input/log/harvester.go
@@ -29,7 +29,6 @@
 package log
 
 import (
-	"bytes"
 	"errors"
 	"fmt"
 	"io"
@@ -283,12 +282,6 @@ func (h *Harvester) Run() error {
 			return nil
 		}
 
-		// Strip UTF-8 BOM if beginning of file
-		// As all BOMS are converted to UTF-8 it is enough to only remove this one
-		if h.state.Offset == 0 {
-			message.Content = bytes.Trim(message.Content, "\xef\xbb\xbf")
-		}
-
 		// Get copy of state to work on
 		// This is important in case sending is not successful so on shutdown
 		// the old offset is reported
diff --git a/libbeat/reader/readfile/encode.go b/libbeat/reader/readfile/encode.go
index 920d9a209209..ada4ae91947b 100644
--- a/libbeat/reader/readfile/encode.go
+++ b/libbeat/reader/readfile/encode.go
@@ -18,6 +18,7 @@
 package readfile
 
 import (
+	"bytes"
 	"io"
 	"time"
 
@@ -53,7 +54,7 @@ func (r EncoderReader) Next() (reader.Message, error) {
 	// Creating message object
 	return reader.Message{
 		Ts:      time.Now(),
-		Content: c,
+		Content: bytes.Trim(c, "\xef\xbb\xbf"),
 		Bytes:   sz,
 	}, err
 }
diff --git a/libbeat/reader/readfile/encode_test.go b/libbeat/reader/readfile/encode_test.go
new file mode 100644
index 000000000000..36d3df433ec5
--- /dev/null
+++ b/libbeat/reader/readfile/encode_test.go
@@ -0,0 +1,73 @@
+// 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.
+
+package readfile
+
+import (
+	"bytes"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+
+	"github.com/elastic/beats/libbeat/reader/readfile/encoding"
+)
+
+func TestEncodeLines(t *testing.T) {
+	testCases := map[string]struct {
+		Input  []byte
+		Output []string
+	}{
+		"simple":            {[]byte("testing simple line\n"), []string{"testing simple line\n"}},
+		"multiline":         {[]byte("testing\nmultiline\n"), []string{"testing\n", "multiline\n"}},
+		"bom-on-first":      {[]byte("\xef\xbb\xbftesting simple line\n"), []string{"testing simple line\n"}},
+		"bom-on-each":       {[]byte("\xef\xbb\xbftesting\n\xef\xbb\xbfmultiline\n"), []string{"testing\n", "multiline\n"}},
+		"bom-in-the-middle": {[]byte("testing simple \xef\xbb\xbfline\n"), []string{"testing simple \xef\xbb\xbfline\n"}},
+	}
+
+	bufferSize := 1000
+	encFactory, ok := encoding.FindEncoding("plain")
+	if !ok {
+		t.Fatal("failed to initiate encoding")
+	}
+
+	for name, testCase := range testCases {
+		t.Run(name, func(t *testing.T) {
+			r := bytes.NewReader(testCase.Input)
+			codec, err := encFactory(r)
+			assert.Nil(t, err, "failed to initialize encoding: %v", err)
+
+			config := Config{
+				Codec:      codec,
+				BufferSize: bufferSize,
+				Terminator: LineFeed,
+			}
+			er, err := NewEncodeReader(r, config)
+			assert.Nil(t, err, "failed to create new encoder: %v", err)
+
+			var output []string
+			for {
+				msg, err := er.Next()
+				if err != nil {
+					break
+				}
+				output = append(output, string(msg.Content))
+			}
+
+			assert.Equal(t, testCase.Output, output)
+		})
+	}
+}