diff --git a/accesstransformers/src/main/java/net/neoforged/jst/accesstransformers/AccessTransformersTransformer.java b/accesstransformers/src/main/java/net/neoforged/jst/accesstransformers/AccessTransformersTransformer.java
index c70f4fb..ec87ce8 100644
--- a/accesstransformers/src/main/java/net/neoforged/jst/accesstransformers/AccessTransformersTransformer.java
+++ b/accesstransformers/src/main/java/net/neoforged/jst/accesstransformers/AccessTransformersTransformer.java
@@ -11,10 +11,14 @@
 import picocli.CommandLine;
 
 import java.io.IOException;
+import java.io.Reader;
 import java.io.UncheckedIOException;
+import java.nio.file.Files;
 import java.nio.file.Path;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 import java.util.concurrent.ConcurrentHashMap;
 
 public class AccessTransformersTransformer implements SourceTransformer {
@@ -25,8 +29,13 @@ public class AccessTransformersTransformer implements SourceTransformer {
     @CommandLine.Option(names = "--access-transformer-validation", description = "The level of validation to use for ats")
     public AccessTransformerValidation validation = AccessTransformerValidation.LOG;
 
+    // TODO: as is, either this or the normal option is required
+    @CommandLine.Option(names = "--access-transformer-no-validation")
+    public List<Path> atFilesWithoutValidation;
+
     private AccessTransformerFiles ats;
     private Map<Target, Transformation> pendingATs;
+    private Set<String> sourcesWithoutValidation;
     private Logger logger;
     private volatile boolean errored;
 
@@ -34,6 +43,7 @@ public class AccessTransformersTransformer implements SourceTransformer {
     public void beforeRun(TransformContext context) {
         ats = new AccessTransformerFiles();
         logger = context.logger();
+        sourcesWithoutValidation = new HashSet<>();
 
         for (Path path : atFiles) {
             try {
@@ -44,20 +54,44 @@ public void beforeRun(TransformContext context) {
             }
         }
 
+        for (Path path : atFilesWithoutValidation) {
+            var sourceName = path.toAbsolutePath().toString();
+            try (Reader reader = Files.newBufferedReader(path)) {
+                ats.loadAT(reader, sourceName);
+            } catch (IOException ex) {
+                logger.error("Failed to parse access transformer file %s: %s", path, ex.getMessage());
+                throw new UncheckedIOException(ex);
+            }
+            sourcesWithoutValidation.add(sourceName);
+        }
+
         pendingATs = new ConcurrentHashMap<>(ats.getAccessTransformers());
     }
 
     @Override
     public boolean afterRun(TransformContext context) {
-        if (!pendingATs.isEmpty()) {
-            pendingATs.forEach((target, transformation) -> {
-                // ClassTarget for inner classes have a corresponding InnerClassTarget which is more obvious for users
-                // so we don't log the ClassTarget as that will cause duplication
-                if (target instanceof Target.ClassTarget && target.className().contains("$")) return;
-                logger.error("Access transformer %s, targeting %s did not apply as its target doesn't exist", transformation, target);
-            });
+        pendingATs.forEach((target, transformation) -> {
+            // Ignore targets that could not be applied,
+            // but are only referenced in AT files for which we don't want to perform any validation
+            boolean ignore = transformation.origins()
+                    .stream()
+                    .allMatch(origin -> {
+                        var colonPos = origin.lastIndexOf(':');
+                        var sourceName = colonPos == -1 ? origin : origin.substring(0, colonPos);
+                        return sourcesWithoutValidation.contains(sourceName);
+                    });
+            if (ignore) {
+                return;
+            }
+            // ClassTarget for inner classes have a corresponding InnerClassTarget which is more obvious for users
+            // so we don't log the ClassTarget as that will cause duplication
+            if (target instanceof Target.ClassTarget && target.className().contains("$")) {
+                return;
+            }
+
+            logger.error("Access transformer %s, targeting %s did not apply as its target doesn't exist", transformation, target);
             errored = true;
-        }
+        });
 
         return !(errored && validation == AccessTransformerValidation.ERROR);
     }
diff --git a/tests/data/accesstransformer/partially_invalid/accesstransformer-checked.cfg b/tests/data/accesstransformer/partially_invalid/accesstransformer-checked.cfg
new file mode 100644
index 0000000..03fbbc4
--- /dev/null
+++ b/tests/data/accesstransformer/partially_invalid/accesstransformer-checked.cfg
@@ -0,0 +1 @@
+public C1
diff --git a/tests/data/accesstransformer/partially_invalid/accesstransformer-unchecked.cfg b/tests/data/accesstransformer/partially_invalid/accesstransformer-unchecked.cfg
new file mode 100644
index 0000000..4ec0c33
--- /dev/null
+++ b/tests/data/accesstransformer/partially_invalid/accesstransformer-unchecked.cfg
@@ -0,0 +1 @@
+public Cdoesnotexist
diff --git a/tests/data/accesstransformer/partially_invalid/expected/C1.java b/tests/data/accesstransformer/partially_invalid/expected/C1.java
new file mode 100644
index 0000000..9784452
--- /dev/null
+++ b/tests/data/accesstransformer/partially_invalid/expected/C1.java
@@ -0,0 +1,3 @@
+public class C1 {
+    C1() {}
+}
diff --git a/tests/data/accesstransformer/partially_invalid/source/C1.java b/tests/data/accesstransformer/partially_invalid/source/C1.java
new file mode 100644
index 0000000..44f95f7
--- /dev/null
+++ b/tests/data/accesstransformer/partially_invalid/source/C1.java
@@ -0,0 +1,2 @@
+class C1 {
+}
diff --git a/tests/src/test/java/net/neoforged/jst/tests/EmbeddedTest.java b/tests/src/test/java/net/neoforged/jst/tests/EmbeddedTest.java
index 365b3c0..ebb2669 100644
--- a/tests/src/test/java/net/neoforged/jst/tests/EmbeddedTest.java
+++ b/tests/src/test/java/net/neoforged/jst/tests/EmbeddedTest.java
@@ -297,6 +297,29 @@ void testIllegal() throws Exception {
         void testFolderClasspathEntries() throws Exception {
             runATTest("folder_classpath_entry", "--classpath=" + testDataRoot.resolve("accesstransformer/folder_classpath_entry/deps"));
         }
+
+        @Test
+        void testPartialValidation() throws Exception {
+            var testDirName = "accesstransformer/partially_invalid";
+            var checkedAtPath = testDataRoot.resolve(testDirName).resolve("accesstransformer-checked.cfg");
+            var uncheckedAtPath = testDataRoot.resolve(testDirName).resolve("accesstransformer-unchecked.cfg");
+            runTest(testDirName, txt -> txt,
+                    "--enable-accesstransformers",
+                    "--access-transformer", checkedAtPath.toString(),
+                    "--access-transformer-no-validation", uncheckedAtPath.toString(),
+                    "--access-transformer-validation=error"
+            );
+
+            // Swapping which file is validated should throw:
+            assertThrows(RuntimeException.class, () -> {
+                runTest(testDirName, txt -> txt,
+                        "--enable-accesstransformers",
+                        "--access-transformer", uncheckedAtPath.toString(),
+                        "--access-transformer-no-validation", checkedAtPath.toString(),
+                        "--access-transformer-validation=error"
+                );
+            });
+        }
     }
 
     @Nested