diff --git a/spring-boot-project/spring-boot-docs/src/docs/asciidoc/spring-boot-features.adoc b/spring-boot-project/spring-boot-docs/src/docs/asciidoc/spring-boot-features.adoc
index 76867dcf99..c1a01de779 100644
--- a/spring-boot-project/spring-boot-docs/src/docs/asciidoc/spring-boot-features.adoc
+++ b/spring-boot-project/spring-boot-docs/src/docs/asciidoc/spring-boot-features.adoc
@@ -886,7 +886,8 @@ For `application.properties` files a special `#---` comment is used to mark the
 	spring.application.name=MyCloudApp
 ----
 
-NOTE: Property file separators must not have any leading or trailing whitespace and must have exactly three hyphen characters.
+NOTE: Property file separators must not have any leading whitespace and must have exactly three hyphen characters.
+The lines immediately before and after the separator must not be comments.
 
 TIP: Multi-document property files are often used in conjunction with activation properties such as `spring.config.activate.on-profile`.
 See the <<boot-features-external-config-file-activation-properties, next section>> for details.
diff --git a/spring-boot-project/spring-boot/src/main/java/org/springframework/boot/env/OriginTrackedPropertiesLoader.java b/spring-boot-project/spring-boot/src/main/java/org/springframework/boot/env/OriginTrackedPropertiesLoader.java
index f84e0c28ec..96ee296bfb 100644
--- a/spring-boot-project/spring-boot/src/main/java/org/springframework/boot/env/OriginTrackedPropertiesLoader.java
+++ b/spring-boot-project/spring-boot/src/main/java/org/springframework/boot/env/OriginTrackedPropertiesLoader.java
@@ -73,46 +73,58 @@ class OriginTrackedPropertiesLoader {
 	 * @throws IOException on read error
 	 */
 	List<Document> load(boolean expandLists) throws IOException {
-		List<Document> result = new ArrayList<>();
+		List<Document> documents = new ArrayList<>();
 		Document document = new Document();
+		StringBuilder buffer = new StringBuilder();
 		try (CharacterReader reader = new CharacterReader(this.resource)) {
-			StringBuilder buffer = new StringBuilder();
 			while (reader.read()) {
 				if (reader.isPoundCharacter()) {
 					if (isNewDocument(reader)) {
 						if (!document.isEmpty()) {
-							result.add(document);
+							documents.add(document);
 						}
 						document = new Document();
 					}
 					else {
+						if (document.isEmpty() && !documents.isEmpty()) {
+							document = documents.remove(documents.size() - 1);
+						}
+						reader.setLastLineComment(true);
 						reader.skipComment();
 					}
 				}
-				String key = loadKey(buffer, reader).trim();
-				if (expandLists && key.endsWith("[]")) {
-					key = key.substring(0, key.length() - 2);
-					int index = 0;
-					do {
-						OriginTrackedValue value = loadValue(buffer, reader, true);
-						document.put(key + "[" + (index++) + "]", value);
-						if (!reader.isEndOfLine()) {
-							reader.read();
-						}
-					}
-					while (!reader.isEndOfLine());
-				}
 				else {
-					OriginTrackedValue value = loadValue(buffer, reader, false);
-					document.put(key, value);
+					reader.setLastLineComment(false);
+					loadKeyAndValue(expandLists, document, reader, buffer);
 				}
 			}
 
 		}
-		if (!document.isEmpty() && !result.contains(document)) {
-			result.add(document);
+		if (!document.isEmpty() && !documents.contains(document)) {
+			documents.add(document);
+		}
+		return documents;
+	}
+
+	private void loadKeyAndValue(boolean expandLists, Document document, CharacterReader reader, StringBuilder buffer)
+			throws IOException {
+		String key = loadKey(buffer, reader).trim();
+		if (expandLists && key.endsWith("[]")) {
+			key = key.substring(0, key.length() - 2);
+			int index = 0;
+			do {
+				OriginTrackedValue value = loadValue(buffer, reader, true);
+				document.put(key + "[" + (index++) + "]", value);
+				if (!reader.isEndOfLine()) {
+					reader.read();
+				}
+			}
+			while (!reader.isEndOfLine());
+		}
+		else {
+			OriginTrackedValue value = loadValue(buffer, reader, false);
+			document.put(key, value);
 		}
-		return result;
 	}
 
 	private String loadKey(StringBuilder buffer, CharacterReader reader) throws IOException {
@@ -149,6 +161,9 @@ class OriginTrackedPropertiesLoader {
 	}
 
 	boolean isNewDocument(CharacterReader reader) throws IOException {
+		if (reader.isLastLineComment()) {
+			return false;
+		}
 		boolean result = reader.getLocation().getColumn() == 0 && reader.isPoundCharacter();
 		result = result && readAndExpect(reader, reader::isHyphenCharacter);
 		result = result && readAndExpect(reader, reader::isHyphenCharacter);
@@ -179,6 +194,8 @@ class OriginTrackedPropertiesLoader {
 
 		private int character;
 
+		private boolean lastLineComment;
+
 		CharacterReader(Resource resource) throws IOException {
 			this.reader = new LineNumberReader(
 					new InputStreamReader(resource.getInputStream(), StandardCharsets.ISO_8859_1));
@@ -222,6 +239,14 @@ class OriginTrackedPropertiesLoader {
 			}
 		}
 
+		private void setLastLineComment(boolean lastLineComment) {
+			this.lastLineComment = lastLineComment;
+		}
+
+		private boolean isLastLineComment() {
+			return this.lastLineComment;
+		}
+
 		private void skipComment() throws IOException {
 			while (this.character != '\n' && this.character != -1) {
 				this.character = this.reader.read();
diff --git a/spring-boot-project/spring-boot/src/test/java/org/springframework/boot/env/OriginTrackedPropertiesLoaderTests.java b/spring-boot-project/spring-boot/src/test/java/org/springframework/boot/env/OriginTrackedPropertiesLoaderTests.java
index e13b4990b0..971c425bfa 100644
--- a/spring-boot-project/spring-boot/src/test/java/org/springframework/boot/env/OriginTrackedPropertiesLoaderTests.java
+++ b/spring-boot-project/spring-boot/src/test/java/org/springframework/boot/env/OriginTrackedPropertiesLoaderTests.java
@@ -286,6 +286,13 @@ class OriginTrackedPropertiesLoaderTests {
 		assertThat(getValue(value)).isEqualTo("trailing ");
 	}
 
+	@Test
+	void existingCommentsAreNotTreatedAsMultiDoc() throws Exception {
+		this.resource = new ClassPathResource("existing-non-multi-document.properties", getClass());
+		this.documents = new OriginTrackedPropertiesLoader(this.resource).load();
+		assertThat(this.documents.size()).isEqualTo(1);
+	}
+
 	private OriginTrackedValue getFromFirst(String key) {
 		return this.documents.get(0).asMap().get(key);
 	}
diff --git a/spring-boot-project/spring-boot/src/test/resources/org/springframework/boot/env/existing-non-multi-document.properties b/spring-boot-project/spring-boot/src/test/resources/org/springframework/boot/env/existing-non-multi-document.properties
new file mode 100644
index 0000000000..b5e003745c
--- /dev/null
+++ b/spring-boot-project/spring-boot/src/test/resources/org/springframework/boot/env/existing-non-multi-document.properties
@@ -0,0 +1,16 @@
+#---
+# Test
+#---
+
+spring=boot
+
+#---
+# Test
+
+boot=bar
+
+
+# Test
+#---
+
+bar=ok