diff --git a/check_api/src/main/java/com/google/errorprone/scanner/ScannerSupplier.java b/check_api/src/main/java/com/google/errorprone/scanner/ScannerSupplier.java
index 92167d27b85..a0294b10198 100644
--- a/check_api/src/main/java/com/google/errorprone/scanner/ScannerSupplier.java
+++ b/check_api/src/main/java/com/google/errorprone/scanner/ScannerSupplier.java
@@ -17,6 +17,7 @@
 package com.google.errorprone.scanner;
 
 import static com.google.common.collect.ImmutableListMultimap.flatteningToImmutableListMultimap;
+import static java.util.function.Predicate.not;
 
 import com.google.common.base.Predicate;
 import com.google.common.base.Supplier;
@@ -298,7 +299,7 @@ public ScannerSupplier plus(ScannerSupplier other) {
   public ScannerSupplier filter(Predicate<? super BugCheckerInfo> predicate) {
     ImmutableSet<String> disabled =
         getAllChecks().values().stream()
-            .filter(predicate.negate())
+            .filter(bci -> disabled().contains(bci.canonicalName()) || !predicate.test(bci))
             .map(BugCheckerInfo::canonicalName)
             .collect(ImmutableSet.toImmutableSet());
     return new ScannerSupplierImpl(getAllChecks(), severities(), disabled, getFlags());
diff --git a/core/src/test/java/com/google/errorprone/ErrorProneJavaCompilerTest.java b/core/src/test/java/com/google/errorprone/ErrorProneJavaCompilerTest.java
index 72cc7fa348d..a8de13a5a9b 100644
--- a/core/src/test/java/com/google/errorprone/ErrorProneJavaCompilerTest.java
+++ b/core/src/test/java/com/google/errorprone/ErrorProneJavaCompilerTest.java
@@ -486,6 +486,32 @@ class StringConstantWrapper {
             """);
   }
 
+  @Test
+  public void patchAllWithDisableAllChecks() throws IOException {
+    JavaFileObject fileObject =
+        createOnDiskFileObject(
+            "StringConstantWrapper.java",
+            """
+            class StringConstantWrapper {
+              String s = "old-value";
+            }
+            """);
+
+    CompilationResult result =
+        doCompile(
+            Collections.singleton(fileObject),
+            Arrays.asList("-XepPatchChecks:", "-XepPatchLocation:IN_PLACE", "-XepDisableAllChecks"),
+            ImmutableList.of(AssignmentUpdater.class));
+    assertThat(result.succeeded).isTrue();
+    assertThat(Files.readString(Path.of(fileObject.toUri())))
+        .isEqualTo(
+            """
+            class StringConstantWrapper {
+              String s = "old-value";
+            }
+            """);
+  }
+
   @Test
   public void patchSingleWithCheckDisabled() throws IOException {
     JavaFileObject fileObject =
diff --git a/core/src/test/java/com/google/errorprone/scanner/ScannerSupplierTest.java b/core/src/test/java/com/google/errorprone/scanner/ScannerSupplierTest.java
index 80c753da94e..20272cbc1c8 100644
--- a/core/src/test/java/com/google/errorprone/scanner/ScannerSupplierTest.java
+++ b/core/src/test/java/com/google/errorprone/scanner/ScannerSupplierTest.java
@@ -243,7 +243,9 @@ public void filterWorks() {
         ScannerSupplier.fromBugCheckerClasses(
             ArrayEquals.class, BadShiftAmount.class, StaticQualifiedUsingExpression.class);
 
-    assertScanner(ss.filter(input -> input.canonicalName().equals("BadShiftAmount")))
+    ScannerSupplier derivedSupplier = ss.filter(input -> !input.canonicalName().startsWith("S"));
+    assertScanner(derivedSupplier).hasEnabledChecks(ArrayEquals.class, BadShiftAmount.class);
+    assertScanner(derivedSupplier.filter(input -> !input.canonicalName().startsWith("A")))
         .hasEnabledChecks(BadShiftAmount.class);
   }