diff --git a/isthmus-cli/build.gradle.kts b/isthmus-cli/build.gradle.kts
index 7a3df32ef..ec1af73a7 100644
--- a/isthmus-cli/build.gradle.kts
+++ b/isthmus-cli/build.gradle.kts
@@ -56,10 +56,9 @@ graalvmNative {
     named("main") {
       imageName.set("isthmus")
       fallback.set(false)
-      buildArgs.add("-H:IncludeResources=.*yaml")
-      buildArgs.add("--report-unsupported-elements-at-runtime")
+      // Resource inclusion and dynamic-proxy configuration are declared in
+      // src/main/resources/META-INF/native-image/.../reachability-metadata.json.
       buildArgs.add("-H:+ReportExceptionStackTraces")
-      buildArgs.add("-H:DynamicProxyConfigurationFiles=${project.file("proxies.json")}")
       buildArgs.add("--features=io.substrait.isthmus.cli.RegisterAtRuntime")
       // Removed due to https://github.com/oracle/graal/issues/13316
       // buildArgs.add("--future-defaults=all")
@@ -98,7 +97,20 @@ tasks.register("writeIsthmusVersion") {
   }
 }
 
-tasks.named("compileJava") { dependsOn("writeIsthmusVersion") }
+tasks.named<JavaCompile>("compileJava") {
+  dependsOn("writeIsthmusVersion")
+  // picocli-codegen emits an empty (`[]`) proxy-config.json because isthmus uses class-based
+  // @Command annotations and needs no JDK dynamic proxies. Its mere presence makes GraalVM emit a
+  // warning, so delete it after compile. reflect-config.json / resource-config.json (the real
+  // picocli metadata) are left untouched.
+  doLast {
+    destinationDirectory
+      .file("META-INF/native-image/picocli-generated/proxy-config.json")
+      .get()
+      .asFile
+      .delete()
+  }
+}
 
 tasks.named<Javadoc>("javadoc") {
   description = "Generate Javadoc for main source files (excludes generated)."
diff --git a/isthmus-cli/proxies.json b/isthmus-cli/proxies.json
deleted file mode 100644
index 19838d6c4..000000000
--- a/isthmus-cli/proxies.json
+++ /dev/null
@@ -1,30 +0,0 @@
-[
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$AllPredicates$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$Collation$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$ColumnOrigin$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$ColumnUniqueness$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$CumulativeCost$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$DistinctRowCount$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$Distribution$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$ExplainVisibility$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$ExpressionLineage$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$FunctionalDependency$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$InputFieldsUsed$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$LowerBoundCost$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$MaxRowCount$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$Measure$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$Memory$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$MinRowCount$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$NodeTypes$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$NonCumulativeCost$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$Parallelism$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$PercentageOriginalRows$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$PopulationSize$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$Predicates$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$RowCount$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$Selectivity$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$Size$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$TableReferences$Handler"],
-  ["org.apache.calcite.rel.metadata.BuiltInMetadata$UniqueKeys$Handler"],
-  ["org.apache.calcite.runtime.CalciteResource"]
-]
diff --git a/isthmus-cli/src/main/resources/META-INF/native-image/io.substrait/isthmus-cli/reachability-metadata.json b/isthmus-cli/src/main/resources/META-INF/native-image/io.substrait/isthmus-cli/reachability-metadata.json
new file mode 100644
index 000000000..a73d84903
--- /dev/null
+++ b/isthmus-cli/src/main/resources/META-INF/native-image/io.substrait/isthmus-cli/reachability-metadata.json
@@ -0,0 +1,206 @@
+{
+  "comment": "GraalVM reachability metadata for the isthmus native image.",
+  "resources": [
+    {
+      "glob": "**/*.yaml"
+    }
+  ],
+  "reflection": [
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$AllPredicates$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$Collation$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$ColumnOrigin$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$ColumnUniqueness$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$CumulativeCost$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$DistinctRowCount$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$Distribution$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$ExplainVisibility$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$ExpressionLineage$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$FunctionalDependency$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$InputFieldsUsed$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$LowerBoundCost$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$MaxRowCount$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$Measure$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$Memory$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$MinRowCount$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$NodeTypes$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$NonCumulativeCost$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$Parallelism$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$PercentageOriginalRows$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$PopulationSize$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$Predicates$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$RowCount$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$Selectivity$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$Size$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$TableReferences$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.rel.metadata.BuiltInMetadata$UniqueKeys$Handler"
+        ]
+      }
+    },
+    {
+      "type": {
+        "proxy": [
+          "org.apache.calcite.runtime.CalciteResource"
+        ]
+      }
+    }
+  ]
+}