diff --git a/spring-boot/src/main/java/org/springframework/boot/logging/log4j2/Log4J2LoggingSystem.java b/spring-boot/src/main/java/org/springframework/boot/logging/log4j2/Log4J2LoggingSystem.java
index 4f88f3ad45..4bcc9c5909 100644
--- a/spring-boot/src/main/java/org/springframework/boot/logging/log4j2/Log4J2LoggingSystem.java
+++ b/spring-boot/src/main/java/org/springframework/boot/logging/log4j2/Log4J2LoggingSystem.java
@@ -125,13 +125,13 @@ public class Log4J2LoggingSystem extends Slf4JLoggingSystem {
 	@Override
 	public void beforeInitialize() {
 		super.beforeInitialize();
-		getLoggerConfig(null).addFilter(FILTER);
+		getRootLoggerConfig().addFilter(FILTER);
 	}
 
 	@Override
 	public void initialize(LoggingInitializationContext initializationContext,
 			String configLocation, LogFile logFile) {
-		getLoggerConfig(null).removeFilter(FILTER);
+		getRootLoggerConfig().removeFilter(FILTER);
 		super.initialize(initializationContext, configLocation, logFile);
 	}
 
@@ -183,15 +183,25 @@ public class Log4J2LoggingSystem extends Slf4JLoggingSystem {
 	}
 
 	@Override
-	public void setLogLevel(String loggerName, LogLevel level) {
-		getLoggerConfig(loggerName).setLevel(LEVELS.get(level));
+	public void setLogLevel(String loggerName, LogLevel logLevel) {
+		Level level = LEVELS.get(logLevel);
+		LoggerConfig loggerConfig = getLoggerConfig(loggerName);
+		if (loggerConfig == null) {
+			loggerConfig = new LoggerConfig(loggerName, level, true);
+			getLoggerContext().getConfiguration().addLogger(loggerName, loggerConfig);
+		}
+		else {
+			loggerConfig.setLevel(level);
+		}
 		getLoggerContext().updateLoggers();
 	}
 
+	private LoggerConfig getRootLoggerConfig() {
+		return getLoggerContext().getConfiguration().getLoggerConfig("");
+	}
+
 	private LoggerConfig getLoggerConfig(String loggerName) {
-		LoggerConfig loggerConfig = getLoggerContext().getConfiguration()
-				.getLoggerConfig(loggerName == null ? "" : loggerName);
-		return loggerConfig;
+		return getLoggerContext().getConfiguration().getLoggers().get(loggerName);
 	}
 
 	private LoggerContext getLoggerContext() {
diff --git a/spring-boot/src/test/java/org/springframework/boot/logging/log4j2/Log4J2LoggingSystemTests.java b/spring-boot/src/test/java/org/springframework/boot/logging/log4j2/Log4J2LoggingSystemTests.java
index 025031331a..2d26aba28b 100644
--- a/spring-boot/src/test/java/org/springframework/boot/logging/log4j2/Log4J2LoggingSystemTests.java
+++ b/spring-boot/src/test/java/org/springframework/boot/logging/log4j2/Log4J2LoggingSystemTests.java
@@ -36,12 +36,13 @@ import org.springframework.util.StringUtils;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 
+import static org.hamcrest.CoreMatchers.containsString;
 import static org.hamcrest.Matchers.arrayContaining;
 import static org.hamcrest.Matchers.equalTo;
 import static org.hamcrest.Matchers.instanceOf;
 import static org.hamcrest.Matchers.is;
+import static org.hamcrest.Matchers.not;
 import static org.hamcrest.Matchers.notNullValue;
-import static org.hamcrest.core.StringContains.containsString;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertThat;
 import static org.junit.Assert.assertTrue;
@@ -130,6 +131,17 @@ public class Log4J2LoggingSystemTests extends AbstractLoggingSystemTests {
 				equalTo(1));
 	}
 
+	@Test
+	public void setLevelOfUnconfiguredLoggerDoesNotAffectRootConfiguration()
+			throws Exception {
+		this.loggingSystem.beforeInitialize();
+		this.loggingSystem.initialize(null, null, null);
+		LogManager.getRootLogger().debug("Hello");
+		this.loggingSystem.setLogLevel("foo.bar.baz", LogLevel.DEBUG);
+		LogManager.getRootLogger().debug("Hello");
+		assertThat(this.output.toString(), not(containsString("Hello")));
+	}
+
 	@Test
 	@Ignore("Fails on Bamboo")
 	public void loggingThatUsesJulIsCaptured() {