diff --git a/changes/47412-render-command-line-flags-as-is b/changes/47412-render-command-line-flags-as-is
new file mode 100644
index 0000000000..769d8bcb7e
--- /dev/null
+++ b/changes/47412-render-command-line-flags-as-is
@@ -0,0 +1 @@
+* Fixed the agent settings YAML editor (global and fleet-level) hiding `command_line_flags` behind a comment when set to `{}` or `null` — those values now render as-is, since they have special semantics (they clear all local osquery flags on hosts).
diff --git a/frontend/utilities/yaml/index.ts b/frontend/utilities/yaml/index.ts
index 6582c95702..f5a5e5b307 100644
--- a/frontend/utilities/yaml/index.ts
+++ b/frontend/utilities/yaml/index.ts
@@ -18,21 +18,20 @@ export const agentOptionsToYaml = (agentOpts: any) => {
     delete agentOpts.overrides;
   }
 
-  // add a comment besides the "command_line_flags" if it is empty
-  let addFlagsComment = false;
-  if (
-    !agentOpts.command_line_flags ||
-    Object.keys(agentOpts.command_line_flags).length === 0
-  ) {
-    // delete it so it does not render, and will add it explicitly after (along with the comment)
-    delete agentOpts.command_line_flags;
-    addFlagsComment = true;
-  }
+  const flagsComment = "# Requires fleetd agent\n";
 
+  // always show the informational comment above "command_line_flags". When
+  // the key is present — even set to {} or null — render it as-is, since
+  // those empty values have special semantics; when absent, suggest it with
+  // a commented-out placeholder.
   let yamlString = yaml.dump(agentOpts);
-  if (addFlagsComment) {
-    yamlString +=
-      "# Requires Fleet's osquery installer\n# command_line_flags: {}\n";
+  if ("command_line_flags" in agentOpts) {
+    yamlString = yamlString.replace(
+      /^command_line_flags:/m,
+      `${flagsComment}command_line_flags:`
+    );
+  } else {
+    yamlString += `${flagsComment}# command_line_flags: {}\n`;
   }
 
   return yamlString;
diff --git a/frontend/utilities/yaml/yaml.tests.ts b/frontend/utilities/yaml/yaml.tests.ts
new file mode 100644
index 0000000000..9da3591829
--- /dev/null
+++ b/frontend/utilities/yaml/yaml.tests.ts
@@ -0,0 +1,52 @@
+import { agentOptionsToYaml } from "utilities/yaml";
+
+const FLAGS_COMMENT = "# Requires fleetd agent\n";
+
+describe("agentOptionsToYaml", () => {
+  it("adds a commented-out placeholder when the command_line_flags key is absent", () => {
+    expect(agentOptionsToYaml({ config: {} })).toContain(
+      `${FLAGS_COMMENT}# command_line_flags: {}\n`
+    );
+  });
+
+  it("adds a commented-out placeholder when agent options are unset", () => {
+    expect(agentOptionsToYaml(null)).toContain(
+      `${FLAGS_COMMENT}# command_line_flags: {}\n`
+    );
+  });
+
+  it("renders command_line_flags set to an empty object as-is, with the comment above it", () => {
+    const result = agentOptionsToYaml({
+      config: {},
+      command_line_flags: {},
+    });
+    expect(result).toContain(`${FLAGS_COMMENT}command_line_flags: {}`);
+    expect(result).not.toContain("# command_line_flags: {}");
+  });
+
+  it("renders command_line_flags set to null as-is, with the comment above it", () => {
+    const result = agentOptionsToYaml({
+      config: {},
+      command_line_flags: null,
+    });
+    expect(result).toContain(`${FLAGS_COMMENT}command_line_flags: null`);
+    expect(result).not.toContain("# command_line_flags: {}");
+  });
+
+  it("renders non-empty command_line_flags with the comment above it", () => {
+    const result = agentOptionsToYaml({
+      config: {},
+      command_line_flags: { verbose: true },
+    });
+    expect(result).toContain(
+      `${FLAGS_COMMENT}command_line_flags:\n  verbose: true`
+    );
+    expect(result).not.toContain("# command_line_flags: {}");
+  });
+
+  it("omits an empty overrides key", () => {
+    expect(agentOptionsToYaml({ config: {}, overrides: {} })).not.toContain(
+      "overrides"
+    );
+  });
+});