diff --git a/scripts/runtime_settings.py b/scripts/runtime_settings.py
index 8878faa..d2d5e5c 100644
--- a/scripts/runtime_settings.py
+++ b/scripts/runtime_settings.py
@@ -64,10 +64,17 @@ class Assignment:
     name: str
     value: str
 
+    @property
+    def deletes_variable(self) -> bool:
+        return self.value == ""
+
     def gh_command(self, *, redact_body: bool = False, redact_metadata: bool = False) -> list[str]:
-        body = redacted_value() if redact_body else self.value
         repository = redacted_value() if redact_metadata else self.repository
-        command = ["gh", "variable", "set", self.name, "--repo", repository, "--body", body]
+        if self.deletes_variable:
+            command = ["gh", "variable", "delete", self.name, "--repo", repository]
+        else:
+            body = redacted_value() if redact_body else self.value
+            command = ["gh", "variable", "set", self.name, "--repo", repository, "--body", body]
         if self.variable_scope == "environment":
             environment = redacted_value() if redact_metadata else (self.environment or "")
             command.extend(["--env", environment])
@@ -91,6 +98,7 @@ def assignment_payload(assignment: Assignment, *, redact_values: bool = False) -
         "variable_scope": assignment.variable_scope,
         "environment": assignment.environment,
         "name": assignment.name,
+        "action": "delete" if assignment.deletes_variable else "set",
         "value": redacted_value() if redact_values else assignment.value,
     }
     if redact_values:
@@ -570,7 +578,24 @@ def command_apply(args: argparse.Namespace) -> int:
         return 0
 
     for assignment in all_assignments:
-        subprocess.run(assignment.gh_command(), check=True)
+        result = subprocess.run(
+            assignment.gh_command(),
+            text=True,
+            capture_output=assignment.deletes_variable,
+            check=False,
+        )
+        if result.returncode == 0:
+            continue
+        if assignment.deletes_variable:
+            detail = f"{result.stderr}\n{result.stdout}".lower()
+            if "not found" in detail or "could not find" in detail or "http 404" in detail:
+                print(f"{assignment.name} was already absent; delete skipped.")
+                continue
+            if result.stderr:
+                print(result.stderr, file=sys.stderr, end="")
+            if result.stdout:
+                print(result.stdout, file=sys.stderr, end="")
+        raise subprocess.CalledProcessError(result.returncode, assignment.gh_command())
     return 0
 
 
diff --git a/tests/test_runtime_settings.py b/tests/test_runtime_settings.py
index 548df86..684e952 100644
--- a/tests/test_runtime_settings.py
+++ b/tests/test_runtime_settings.py
@@ -101,6 +101,33 @@ def test_assignment_shell_command_can_redact_body_and_metadata(self):
         self.assertNotIn(assignment.repository, command)
         self.assertNotIn(assignment.environment, command)
 
+    def test_empty_assignment_deletes_variable_instead_of_setting_empty_body(self):
+        assignment = runtime_settings.Assignment(
+            "longbridge/sg",
+            "QuantStrategyLab/LongBridgePlatform",
+            "environment",
+            "longbridge-sg",
+            "LONGBRIDGE_MIN_RESERVED_CASH_USD",
+            "",
+        )
+
+        self.assertTrue(assignment.deletes_variable)
+        self.assertEqual(
+            assignment.gh_command(),
+            [
+                "gh",
+                "variable",
+                "delete",
+                "LONGBRIDGE_MIN_RESERVED_CASH_USD",
+                "--repo",
+                "QuantStrategyLab/LongBridgePlatform",
+                "--env",
+                "longbridge-sg",
+            ],
+        )
+        self.assertNotIn("--body", assignment.shell_command())
+        self.assertEqual(runtime_settings.assignment_payload(assignment)["action"], "delete")
+
     def test_plugin_mount_schema_version_must_be_non_empty_string(self):
         _, target = self.load_target("examples/targets/schwab/live.example.json")
         target["plugin_mounts"][0]["expected_schema_version"] = ""