diff --git a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
index 8afe696f9..0442d6566 100644
--- a/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
+++ b/plugin/src/main/java/org/openrewrite/gradle/isolated/DefaultProjectParser.java
@@ -268,7 +268,7 @@ private static StringBuilder repeat(int repeat) {
 
     public Collection<Path> listSources() {
         // Use a sorted collection so that gradle input detection isn't thrown off by ordering
-        Set<Path> result = new TreeSet<>(omniParser(emptySet()).acceptedPaths(project.getProjectDir().toPath()));
+        Set<Path> result = new TreeSet<>(omniParser(emptySet()).build().acceptedPaths(baseDir, project.getProjectDir().toPath()));
         //noinspection deprecation
         JavaPluginConvention javaConvention = project.getConvention().findPlugin(JavaPluginConvention.class);
         if (javaConvention != null) {
@@ -292,6 +292,7 @@ public void dryRun(Path reportPath, boolean dumpGcActivity, Consumer<Throwable>
                 heapMetrics.bindTo(meterRegistry);
                 new JvmMemoryMetrics().bindTo(meterRegistry);
 
+                //noinspection deprecation
                 File rewriteBuildDir = new File(project.getBuildDir(), "/rewrite");
                 if (rewriteBuildDir.exists() || rewriteBuildDir.mkdirs()) {
                     File rewriteGcLog = new File(rewriteBuildDir, "rewrite-gc.csv");
@@ -715,6 +716,7 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
                             .map(Supplier::get)
                             .flatMap(jp -> jp.parse(javaPaths, baseDir, ctx))
                             .map(cu -> {
+                                //noinspection deprecation
                                 if (isExcluded(exclusions, cu.getSourcePath()) ||
                                     cu.getSourcePath().startsWith(baseDir.relativize(subproject.getBuildDir().toPath()))) {
                                     return null;
@@ -804,12 +806,13 @@ public Stream<SourceFile> parse(Project subproject, Set<Path> alreadyParsed, Exe
 
                 for (File resourcesDir : sourceSet.getResources().getSourceDirectories()) {
                     if (resourcesDir.exists()) {
-                        OmniParser omniParser = omniParser(alreadyParsed);
-                        List<Path> accepted = omniParser.acceptedPaths(resourcesDir.toPath());
+                        OmniParser omniParser = omniParser(alreadyParsed).build();
+                        List<Path> accepted = omniParser.acceptedPaths(baseDir, resourcesDir.toPath());
                         sourceSetSourceFiles = Stream.concat(
                                 sourceSetSourceFiles,
-                                omniParser.parse(accepted, resourcesDir.toPath(), new InMemoryExecutionContext())
+                                omniParser.parse(accepted, baseDir, new InMemoryExecutionContext())
                         );
+                        alreadyParsed.addAll(accepted);
                         sourceSetSize += accepted.size();
                     }
                 }
@@ -936,13 +939,14 @@ private SourceFileStream parseGradleFiles(
 
     protected SourceFileStream parseNonProjectResources(Project subproject, Set<Path> alreadyParsed, ExecutionContext ctx, List<Marker> projectProvenance, Stream<SourceFile> sourceFiles) {
         //Collect any additional yaml/properties/xml files that are NOT already in a source set.
-        OmniParser omniParser = omniParser(alreadyParsed);
-        List<Path> accepted = omniParser.acceptedPaths(subproject.getProjectDir().toPath());
-        return SourceFileStream.build("", s -> {
-        }).concat(omniParser.parse(accepted, subproject.getProjectDir().toPath(), ctx), accepted.size());
+        OmniParser omniParser = omniParser(alreadyParsed)
+                .build();
+        List<Path> accepted = omniParser.acceptedPaths(baseDir, subproject.getProjectDir().toPath());
+        return SourceFileStream.build("", s -> {})
+                .concat(omniParser.parse(accepted, baseDir, ctx), accepted.size());
     }
 
-    private OmniParser omniParser(Set<Path> alreadyParsed) {
+    private OmniParser.Builder omniParser(Set<Path> alreadyParsed) {
         return OmniParser.builder(
                         OmniParser.RESOURCE_PARSERS,
                         PlainTextParser.builder()
@@ -952,8 +956,7 @@ private OmniParser omniParser(Set<Path> alreadyParsed) {
                 )
                 .exclusionMatchers(pathMatchers(baseDir, mergeExclusions(project, baseDir, extension)))
                 .exclusions(alreadyParsed)
-                .sizeThresholdMb(extension.getSizeThresholdMb())
-                .build();
+                .sizeThresholdMb(extension.getSizeThresholdMb());
     }
 
     private static Collection<String> mergeExclusions(Project project, Path baseDir, RewriteExtension extension) {
diff --git a/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt b/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt
index 41cd37646..fd3052a85 100644
--- a/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt
+++ b/plugin/src/test/kotlin/org/openrewrite/gradle/RewriteRunTest.kt
@@ -156,12 +156,12 @@ class RewriteRunTest : RewritePluginTest {
     }
 
     @Test
-    fun `rewriteRun applies built-in AutoFormat to a multi-project build`(
+    fun `rewriteRun applies recipe to a multi-project build`(
         @TempDir projectDir: File
     ) {
         val bTestClassExpected = """
                 package com.foo;
-    
+                
                 import org.junit.Test;
                 
                 public class BTestClass {
@@ -171,6 +171,15 @@ class RewriteRunTest : RewritePluginTest {
                 }
         """.trimIndent()
         gradleProject(projectDir) {
+            rewriteYaml("""
+                type: specs.openrewrite.org/v1beta/recipe
+                name: org.openrewrite.FormatAndAddProperty
+                recipeList:
+                  - org.openrewrite.java.format.AutoFormat
+                  - org.openrewrite.properties.ChangePropertyKey:
+                      oldPropertyKey: foo
+                      newPropertyKey: bar
+            """)
             buildGradle("""
                 plugins {
                     id("org.openrewrite.rewrite")
@@ -178,7 +187,7 @@ class RewriteRunTest : RewritePluginTest {
                 }
                 
                 rewrite {
-                    activeRecipe("org.openrewrite.java.format.AutoFormat")
+                    activeRecipe("org.openrewrite.FormatAndAddProperty")
                     exclusion("**/BTestClass.java")
                 }
                 
@@ -216,6 +225,7 @@ class RewriteRunTest : RewritePluginTest {
                             public void passes() { }
                         }
                     """)
+                    propertiesFile("test.properties", "foo=baz\n")
                 }
             }
             subproject("b") {
@@ -231,7 +241,7 @@ class RewriteRunTest : RewritePluginTest {
         //language=java
         val aTestClassExpected = """
             package com.foo;
-
+            
             import org.junit.Test;
             
             public class ATestClass {
@@ -245,6 +255,9 @@ class RewriteRunTest : RewritePluginTest {
         assertThat(aTestClassFile.readText()).isEqualTo(aTestClassExpected)
         val bTestClassFile = File(projectDir, "b/src/test/java/com/foo/BTestClass.java")
         assertThat(bTestClassFile.readText()).isEqualTo(bTestClassExpected)
+
+        val propertiesFile = File(projectDir, "a/src/test/resources/test.properties")
+        assertThat(propertiesFile.readText()).isEqualTo("bar=baz\n")
     }
 
     @Suppress("ClassInitializerMayBeStatic", "StatementWithEmptyBody", "ConstantConditions")