diff --git a/check_api/src/main/java/com/google/errorprone/BaseErrorProneJavaCompiler.java b/check_api/src/main/java/com/google/errorprone/BaseErrorProneJavaCompiler.java
index eff5d443bc91..51cf7c94f95b 100644
--- a/check_api/src/main/java/com/google/errorprone/BaseErrorProneJavaCompiler.java
+++ b/check_api/src/main/java/com/google/errorprone/BaseErrorProneJavaCompiler.java
@@ -224,14 +224,12 @@ static ErrorProneAnalyzer createAnalyzer(
             .customRefactorer()
             .or(
                 () -> {
-                  ScannerSupplier toUse =
-                      ErrorPronePlugins.loadPlugins(scannerSupplier, context)
-                          .applyOverrides(epOptions);
+                  ScannerSupplier toUse = ErrorPronePlugins.loadPlugins(scannerSupplier, context);
                   ImmutableSet<String> namedCheckers = epOptions.patchingOptions().namedCheckers();
                   if (!namedCheckers.isEmpty()) {
                     toUse = toUse.filter(bci -> namedCheckers.contains(bci.canonicalName()));
                   }
-                  return ErrorProneScannerTransformer.create(toUse.get());
+                  return ErrorProneScannerTransformer.create(toUse.applyOverrides(epOptions).get());
                 })
             .get();
 
diff --git a/core/src/test/java/com/google/errorprone/scanner/ScannerTest.java b/core/src/test/java/com/google/errorprone/scanner/ScannerTest.java
index 39648b552df1..0a1a1899c8f7 100644
--- a/core/src/test/java/com/google/errorprone/scanner/ScannerTest.java
+++ b/core/src/test/java/com/google/errorprone/scanner/ScannerTest.java
@@ -95,6 +95,22 @@ public void suppressionAnnotationIgnoredWithOptions() {
         .doTest();
   }
 
+  @Test
+  public void dontRunPatchForDisabledChecks() {
+    compilationHelper
+        .addSourceLines(
+            "Test.java",
+            "import com.google.errorprone.scanner.ScannerTest.Foo;",
+            "class Test {",
+            "  Foo foo;",
+            "}")
+        .setArgs(
+            "-XepPatchLocation:IN_PLACE",
+            "-XepPatchChecks:ShouldNotUseFoo",
+            "-Xep:ShouldNotUseFoo:OFF")
+        .doTest();
+  }
+
   @OkToUseFoo // Foo can use itself. But this shouldn't suppress errors on *usages* of Foo.
   public static final class Foo<T> {}