diff --git a/spring-integration-core/src/main/java/org/springframework/integration/store/MessageStore.java b/spring-integration-core/src/main/java/org/springframework/integration/store/MessageStore.java
index 503e05b1fd8..1e8060947ff 100644
--- a/spring-integration-core/src/main/java/org/springframework/integration/store/MessageStore.java
+++ b/spring-integration-core/src/main/java/org/springframework/integration/store/MessageStore.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2002-2019 the original author or authors.
+ * Copyright 2002-2023 the original author or authors.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -62,11 +62,12 @@ public interface MessageStore {
 	<T> Message<T> addMessage(Message<T> message);
 
 	/**
-	 * Remove the Message with the given id from the MessageStore, if present, and return it. If no Message with that id
-	 * is present in the store, this will return <i>null</i>.
-	 *
-	 * @param id THe message identifier.
-	 * @return The message.
+	 * Remove the Message with the given id from the MessageStore, if present, and return it.
+	 * If no Message with that id is present in the store, this will return {@code null}.
+	 * If this method is implemented on a {@link MessageGroupStore},
+	 * the message is removed from the store only if no groups holding this message.
+	 * @param id the message identifier.
+	 * @return the message (if any).
 	 */
 	Message<?> removeMessage(UUID id);
 
diff --git a/spring-integration-jdbc/src/main/java/org/springframework/integration/jdbc/store/JdbcMessageStore.java b/spring-integration-jdbc/src/main/java/org/springframework/integration/jdbc/store/JdbcMessageStore.java
index 26f1fb8c148..2f9b2150b26 100644
--- a/spring-integration-jdbc/src/main/java/org/springframework/integration/jdbc/store/JdbcMessageStore.java
+++ b/spring-integration-jdbc/src/main/java/org/springframework/integration/jdbc/store/JdbcMessageStore.java
@@ -172,6 +172,9 @@ SELECT COUNT(MESSAGE_ID)
 		DELETE_MESSAGE("""
 				DELETE from %PREFIX%MESSAGE
 				where MESSAGE_ID=? and REGION=?
+					and MESSAGE_ID not in (
+										SELECT MESSAGE_ID from %PREFIX%GROUP_TO_MESSAGE
+													where MESSAGE_ID=? and REGION = ?)
 				"""),
 
 		CREATE_MESSAGE("""
@@ -199,7 +202,12 @@ SELECT COUNT(GROUP_KEY)
 
 		DELETE_MESSAGES_FROM_GROUP("""
 				DELETE from %PREFIX%MESSAGE
-				where MESSAGE_ID in (SELECT MESSAGE_ID from %PREFIX%GROUP_TO_MESSAGE where GROUP_KEY = ? and REGION = ?)
+				where MESSAGE_ID in (
+								SELECT MESSAGE_ID from %PREFIX%GROUP_TO_MESSAGE where GROUP_KEY = ? and REGION = ?
+												and MESSAGE_ID not in (
+																SELECT MESSAGE_ID from %PREFIX%GROUP_TO_MESSAGE
+																			where GROUP_KEY != ? and REGION = ?)
+								)
 					and REGION = ?
 				"""),
 
@@ -384,7 +392,8 @@ public Message<?> removeMessage(UUID id) {
 		if (message == null) {
 			return null;
 		}
-		int updated = this.jdbcTemplate.update(getQuery(Query.DELETE_MESSAGE), getKey(id), this.region);
+		String key = getKey(id);
+		int updated = this.jdbcTemplate.update(getQuery(Query.DELETE_MESSAGE), key, this.region, key, this.region);
 		if (updated != 0) {
 			return message;
 		}
@@ -575,15 +584,18 @@ public void removeMessagesFromGroup(Object groupId, Collection<Message<?>> messa
 				(ps, messageToRemove) -> {
 					ps.setString(1, groupKey); // NOSONAR - magic number
 					ps.setString(2, getKey(messageToRemove.getHeaders().getId())); // NOSONAR - magic number
-					ps.setString(3, JdbcMessageStore.this.region); // NOSONAR - magic number
+					ps.setString(3, this.region); // NOSONAR - magic number
 				});
 
 		this.jdbcTemplate.batchUpdate(getQuery(Query.DELETE_MESSAGE),
 				messages,
 				getRemoveBatchSize(),
 				(ps, messageToRemove) -> {
-					ps.setString(1, getKey(messageToRemove.getHeaders().getId())); // NOSONAR - magic number
-					ps.setString(2, JdbcMessageStore.this.region); // NOSONAR - magic number
+					String key = getKey(messageToRemove.getHeaders().getId());
+					ps.setString(1, key); // NOSONAR - magic number
+					ps.setString(2, this.region); // NOSONAR - magic number
+					ps.setString(3, key); // NOSONAR - magic number
+					ps.setString(4, this.region); // NOSONAR - magic number
 				});
 
 		updateMessageGroup(groupKey);
@@ -593,7 +605,8 @@ public void removeMessagesFromGroup(Object groupId, Collection<Message<?>> messa
 	public void removeMessageGroup(Object groupId) {
 		String groupKey = getKey(groupId);
 
-		this.jdbcTemplate.update(getQuery(Query.DELETE_MESSAGES_FROM_GROUP), groupKey, this.region, this.region);
+		this.jdbcTemplate.update(getQuery(Query.DELETE_MESSAGES_FROM_GROUP),
+				groupKey, this.region, groupKey, this.region, this.region);
 
 		if (logger.isDebugEnabled()) {
 			logger.debug("Removing relationships for the group with group key=" + groupKey);
diff --git a/spring-integration-jdbc/src/test/java/org/springframework/integration/jdbc/mysql/MySqlJdbcMessageStoreTests.java b/spring-integration-jdbc/src/test/java/org/springframework/integration/jdbc/mysql/MySqlJdbcMessageStoreTests.java
index 979ad02c7bb..1f8f5d67eff 100644
--- a/spring-integration-jdbc/src/test/java/org/springframework/integration/jdbc/mysql/MySqlJdbcMessageStoreTests.java
+++ b/spring-integration-jdbc/src/test/java/org/springframework/integration/jdbc/mysql/MySqlJdbcMessageStoreTests.java
@@ -497,6 +497,36 @@ public void testMessageGroupCondition() {
 		assertThat(this.messageStore.getMessageGroup(groupId).getCondition()).isEqualTo("testCondition");
 	}
 
+	@Test
+	public void sameMessageInTwoGroupsNotRemovedByFirstGroup() {
+		GenericMessage<String> testMessage = new GenericMessage<>("test data");
+
+		messageStore.addMessageToGroup("1", testMessage);
+		messageStore.addMessageToGroup("2", testMessage);
+
+		messageStore.removeMessageGroup("1");
+
+		assertThat(messageStore.getMessageCount()).isEqualTo(1);
+
+		messageStore.removeMessageGroup("2");
+
+		assertThat(messageStore.getMessageCount()).isEqualTo(0);
+	}
+
+	@Test
+	public void removeMessagesFromGroupDontRemoveSameMessageInOtherGroup() {
+		GenericMessage<String> testMessage = new GenericMessage<>("test data");
+
+		messageStore.addMessageToGroup("1", testMessage);
+		messageStore.addMessageToGroup("2", testMessage);
+
+		messageStore.removeMessagesFromGroup("1", testMessage);
+
+		assertThat(messageStore.getMessageCount()).isEqualTo(1);
+		assertThat(messageStore.messageGroupSize("1")).isEqualTo(0);
+		assertThat(messageStore.messageGroupSize("2")).isEqualTo(1);
+	}
+
 	@Configuration
 	public static class Config {