diff --git a/src/main/java/com/google/devtools/build/lib/skyframe/SkymeldModule.java b/src/main/java/com/google/devtools/build/lib/skyframe/SkymeldModule.java
index ef2facbd2d2824..ca8f1899f24f89 100644
--- a/src/main/java/com/google/devtools/build/lib/skyframe/SkymeldModule.java
+++ b/src/main/java/com/google/devtools/build/lib/skyframe/SkymeldModule.java
@@ -31,13 +31,13 @@ boolean determineIfMergingAnalysisExecution(CommandEnvironment env) {
     PathPackageLocator packageLocator = env.getPackageLocator();
     BuildRequestOptions buildRequestOptions =
         env.getOptions().getOptions(BuildRequestOptions.class);
+    boolean plainValueFromFlag = getPlainValueFromFlag(buildRequestOptions);
     // --nobuild means no execution will be carried out, hence it doesn't make sense to interleave
     // analysis and execution in that case and --experimental_merged_skyframe_analysis_execution
     // should be ignored.
     // Aquery and Cquery implicitly set --nobuild, so there's no need to have a warning here: it
     // makes no different from the users' perspective.
-    if (buildRequestOptions != null
-        && buildRequestOptions.mergedSkyframeAnalysisExecutionDoNotUseDirectly
+    if (plainValueFromFlag
         && !buildRequestOptions.performExecutionPhase
         && !(commandName.equals("aquery") || commandName.equals("cquery"))) {
       env.getReporter()
@@ -46,7 +46,15 @@ boolean determineIfMergingAnalysisExecution(CommandEnvironment env) {
                   "--experimental_merged_skyframe_analysis_execution is incompatible with --nobuild"
                       + " and will be ignored."));
     }
-    boolean plainValueFromFlag = getPlainValueFromFlag(buildRequestOptions);
+    // TODO(b/245922903): Make --explain compatible with Skymeld.
+    if (plainValueFromFlag && buildRequestOptions.explanationPath != null) {
+      env.getReporter()
+          .handle(
+              Event.warn(
+                  "--experimental_merged_skyframe_analysis_execution is incompatible with --explain"
+                      + " and will be ignored."));
+    }
+
     boolean havingMultiPackagePath =
         packageLocator != null && packageLocator.getPathEntries().size() > 1;
     // TODO(b/246324830): Skymeld and multi-package_path are incompatible.
@@ -61,6 +69,7 @@ boolean determineIfMergingAnalysisExecution(CommandEnvironment env) {
     }
     return plainValueFromFlag
         && buildRequestOptions.performExecutionPhase
+        && buildRequestOptions.explanationPath == null
         && !havingMultiPackagePath;
   }
 
diff --git a/src/test/java/com/google/devtools/build/lib/buildtool/SkymeldBuildIntegrationTest.java b/src/test/java/com/google/devtools/build/lib/buildtool/SkymeldBuildIntegrationTest.java
index 7a0ec6e18abed0..c26cfd75ca394a 100644
--- a/src/test/java/com/google/devtools/build/lib/buildtool/SkymeldBuildIntegrationTest.java
+++ b/src/test/java/com/google/devtools/build/lib/buildtool/SkymeldBuildIntegrationTest.java
@@ -475,10 +475,22 @@ public void targetWithNoConfiguration_success() throws Exception {
     assertThat(result.getSuccess()).isTrue();
   }
 
+  @Test
+  public void explain_ignoreSkymeldWithWarning() throws Exception {
+    addOptions("--explain=/dev/null");
+    write("foo/BUILD", "genrule(name = 'foo', outs = ['foo.out'], cmd = 'touch $@')");
+    BuildResult buildResult = buildTarget("//foo");
+
+    assertThat(buildResult.getSuccess()).isTrue();
+
+    events.assertContainsWarning(
+        "--experimental_merged_skyframe_analysis_execution is incompatible with --explain");
+    events.assertContainsWarning("and will be ignored.");
+  }
+
   @Test
   public void multiplePackagePath_ignoreSkymeldWithWarning() throws Exception {
     write("foo/BUILD", "genrule(name = 'foo', outs = ['foo.out'], cmd = 'touch $@')");
-    // write("foo/root.sh");
     write("otherroot/bar/BUILD", "genrule(name = 'bar', outs = ['bar.out'], cmd = 'touch $@')");
     addOptions("--package_path=%workspace%:otherroot");