diff --git a/src/application/SetupRegistrationEnvironment.ts b/src/application/SetupRegistrationEnvironment.ts
index f531c6ffb0..fff31b3223 100644
--- a/src/application/SetupRegistrationEnvironment.ts
+++ b/src/application/SetupRegistrationEnvironment.ts
@@ -7,6 +7,7 @@ const SELECTED_REGISTRATION_SETTINGS = [
   "GHIDRA_MAXMEM",
   "JAVA_HOME",
   "HOPPER_LAUNCHER_PATH",
+  "HOPPER_LOADER_ARGS_JSON",
   "REA_ILSPY_CMD_PATH",
   "REA_ADB_PATH",
   "REA_APKTOOL_COMMAND",
diff --git a/tests/acceptance/setup/registrationRuntimeEnvironmentCli.test.ts b/tests/acceptance/setup/registrationRuntimeEnvironmentCli.test.ts
index 6d9bdfd20c..edbeb257a3 100644
--- a/tests/acceptance/setup/registrationRuntimeEnvironmentCli.test.ts
+++ b/tests/acceptance/setup/registrationRuntimeEnvironmentCli.test.ts
@@ -26,6 +26,7 @@ cliTest(
     const config = join(home, ".qwen/settings.json");
     const selected = {
       HOPPER_LAUNCHER_PATH: join(home, "missing-hopper"),
+      HOPPER_LOADER_ARGS_JSON: '["", "--loader", "Mach-O"]',
       GHIDRA_INSTALL_DIR: join(home, "offline-ghidra"),
       GHIDRA_HEADLESS_MAXMEM: "512M",
       GHIDRA_MAXMEM: "3G",
@@ -111,6 +112,8 @@ cliTest(
     environment.REA_MCP_TOOL_FAMILIES = selected.REA_MCP_TOOL_FAMILIES;
     selected.REA_OBJDUMP_COMMAND = join(home, "replacement-objdump");
     environment.REA_OBJDUMP_COMMAND = selected.REA_OBJDUMP_COMMAND;
+    selected.HOPPER_LOADER_ARGS_JSON = "[]";
+    environment.HOPPER_LOADER_ARGS_JSON = selected.HOPPER_LOADER_ARGS_JSON;
     // Empty headless heap explicitly selects the lower-priority caller value.
     selected.GHIDRA_HEADLESS_MAXMEM = "";
     selected.GHIDRA_MAXMEM = "768M";
diff --git a/tests/boundary/setup/setupLoaderEnvironment.test.ts b/tests/boundary/setup/setupLoaderEnvironment.test.ts
new file mode 100644
index 0000000000..4eb80caad9
--- /dev/null
+++ b/tests/boundary/setup/setupLoaderEnvironment.test.ts
@@ -0,0 +1,74 @@
+import { mkdir, readFile, writeFile } from "node:fs/promises";
+import { join } from "node:path";
+import { expect, it } from "vitest";
+import { createCli } from "../../../src/cli.js";
+import { parseConfig } from "../../../src/config/parseConfig.js";
+import { createTestTempDirectory } from "../../fixtures/temporaryDirectory.js";
+
+it("setup carries explicit Hopper loader selections into Cursor without persisting target or unrelated settings", async () => {
+  const home = await createTestTempDirectory("rea-setup-loader-environment-");
+  const path = join(home, ".cursor/mcp.json");
+  await mkdir(join(home, ".cursor"));
+  await writeFile(path, '{"caller":"retain"}\n');
+  const environment = {
+    HOME: home,
+    USERPROFILE: home,
+    HOPPER_LAUNCHER_PATH: join(home, "missing-hopper"),
+    GHIDRA_INSTALL_DIR: join(home, "missing-ghidra"),
+    JAVA_HOME: join(home, "missing-java"),
+    HOPPER_LOADER_ARGS_JSON: '["", "--loader", "Mach-O"]',
+    HOPPER_TARGET_PATH: join(home, "per-target"),
+    HOPPER_TARGET_KIND: "executable",
+    CALLER_UNRELATED_SETTING: "do not persist",
+  };
+  const setup = async () => {
+    let stdout = "";
+    await createCli(environment).serve(
+      ["setup", "--client", "cursor", "--skill=false", "--yes", "--json"],
+      {
+        env: environment,
+        stdout: (chunk) => {
+          stdout += chunk;
+        },
+        exit: () => undefined,
+      },
+    );
+    return JSON.parse(stdout) as unknown;
+  };
+  const loaderFromSavedRegistration = async () => {
+    const document = JSON.parse(await readFile(path, "utf8"));
+    expect(document.caller).toBe("retain");
+    const saved = document.mcpServers.rea.env;
+    expect(saved).not.toHaveProperty("CALLER_UNRELATED_SETTING");
+    expect(saved).not.toHaveProperty("HOPPER_TARGET_PATH");
+    expect(saved).not.toHaveProperty("HOPPER_TARGET_KIND");
+    const config = parseConfig(saved);
+    if (!config.ok) throw config.error;
+    return config.value.hopperLoaderArgs;
+  };
+
+  expect(await setup()).toMatchObject({ status: "ready" });
+  expect(await loaderFromSavedRegistration()).toEqual([
+    "",
+    "--loader",
+    "Mach-O",
+  ]);
+  const created = await readFile(path, "utf8");
+  expect(JSON.parse(created).mcpServers.rea.env.HOPPER_LOADER_ARGS_JSON).toBe(
+    environment.HOPPER_LOADER_ARGS_JSON,
+  );
+  environment.HOPPER_LOADER_ARGS_JSON = "[]";
+  expect(await setup()).toMatchObject({ status: "ready" });
+  expect(await loaderFromSavedRegistration()).toEqual([]);
+  const updated = await readFile(path, "utf8");
+  expect(JSON.parse(updated).mcpServers.rea.env.HOPPER_LOADER_ARGS_JSON).toBe(
+    "[]",
+  );
+  environment.HOPPER_LOADER_ARGS_JSON = "{";
+  expect(await setup()).toMatchObject({
+    status: "needs_human",
+    plannedActions: [],
+    appliedActions: [],
+  });
+  expect(await readFile(path, "utf8")).toBe(updated);
+});