diff --git a/CHANGELOG.md b/CHANGELOG.md
index b19335f..082ec5b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -26,6 +26,7 @@ Types of changes:
 ### Removed
 
 ### Fixed
+- Fixed `unroll(consolidate_qubits=True)` emitting two unrelated address spaces for a program mixing declared registers with physical qubits — a consolidated register plus as-written `$n` references. Such programs now raise a `ValidationError` naming the physical qubits, and a program using only physical qubits no longer receives an internal register declaration nothing references. ([#353](https://github.com/qBraid/pyqasm/issues/353))
 - Fixed inaccurate `device_qubits` entry in `QasmModule.unroll()` docstring ([#349](https://github.com/qBraid/pyqasm/pull/349))
 - Fixed `remove_idle_qubits()` and `reverse_qubit_order()` ignoring statements nested inside `box` and `if` blocks. Top-level operands were rewritten while nested ones kept their old indices, so the result silently addressed the wrong qubits — and when a nested index fell outside the shrunken register, the output was not a loadable program at all. Both passes now walk nested bodies, as do `has_measurements()` / `remove_measurements()` and `has_barriers()` / `remove_barriers()`; a box left empty by a removal is dropped, since pyqasm rejects a box with no statements. Two consequences of the same blind spot are fixed alongside: a qubit operated on only inside an `if` block no longer counts as idle, and `remove_idle_qubits()` no longer raises `AssertionError` on a program that mixes physical qubits with declared registers. ([#345](https://github.com/qBraid/pyqasm/pull/345))
 - Fixed `unroll(consolidate_qubits=True)` raising `AttributeError: 'str' object has no attribute 'name'` for any gate applied to a physical qubit, e.g. `h $1;`. Consolidation assumed every gate operand was an `IndexedIdentifier`, but a physical qubit survives unrolling as `Identifier("$1")`. Physical qubits are absolute hardware indices belonging to no declared register, so they are now left as written — matching how `measure`, `reset` and `barrier` already treat them. ([#344](https://github.com/qBraid/pyqasm/pull/344))
diff --git a/src/pyqasm/visitor.py b/src/pyqasm/visitor.py
index ea9f5f3..592a724 100644
--- a/src/pyqasm/visitor.py
+++ b/src/pyqasm/visitor.py
@@ -496,8 +496,9 @@ def _qubit_register_consolidation(
 
         Raises:
             ValidationError: If the total number of qubits exceeds the available device qubits,
-                             or if the reserved register '__PYQASM_QUBITS__' is already declared
-                             in the original QASM program.
+                             if the reserved register '__PYQASM_QUBITS__' is already declared
+                             in the original QASM program, or if the program mixes declared
+                             registers with physical qubits.
         """
         if total_qubits > self._module._device_qubits:  # type: ignore
             raise_qasm3_error(
@@ -505,6 +506,23 @@ def _qubit_register_consolidation(
                 f"Total qubits '({total_qubits})' exceed device qubits '({self._module._device_qubits})'.",
             )
 
+        # physical qubits are kept as written, so consolidating around them would emit
+        # two address spaces the output cannot relate (issue #353)
+        physical_qubits = sorted(
+            name for name, _ in self._module._qubit_depths if name.startswith("$")
+        )
+        if physical_qubits:
+            # presence, not capacity: a zero-sized declared register still declares
+            # a second address space
+            if self._global_qreg_size_map:
+                raise_qasm3_error(
+                    "Cannot consolidate qubit registers: the program mixes declared "
+                    f"registers with physical qubits ({', '.join(physical_qubits)})",
+                )
+            # only physical qubits: nothing to consolidate, so do not declare an
+            # internal register nothing would reference
+            return unrolled_stmts
+
         global_scope = self._scope_manager.get_global_scope()
         for var, val in global_scope.items():
             if var == INTERNAL_QUBIT_REGISTER:
diff --git a/tests/qasm3/test_device_qubits.py b/tests/qasm3/test_device_qubits.py
index 7389633..3a97569 100644
--- a/tests/qasm3/test_device_qubits.py
+++ b/tests/qasm3/test_device_qubits.py
@@ -331,41 +331,66 @@ def test_incorrect_qubit_reg(qasm_code, error_message, error_span, caplog):
     assert error_span in caplog.text
 
 
-def test_physical_qubits_are_not_consolidated():
-    """Physical qubits are absolute hardware indices and belong to no declared register,
-    so consolidation must leave them alone instead of raising (see #343)."""
-    qasm = """OPENQASM 3.0;
+@pytest.mark.parametrize(
+    "operation",
+    [
+        "cz $2, q[1];",
+        "c = measure $2;",
+        "reset $2;",
+        "barrier $2;",
+    ],
+)
+def test_mixed_declared_and_physical_rejected_when_consolidating(operation):
+    """A program mixing declared registers with physical qubits would consolidate into
+    two address spaces the output cannot relate, so it is rejected (issue #353)."""
+    qasm = f"""OPENQASM 3.0;
     include "stdgates.inc";
     qubit[2] q;
     bit c;
     h q[0];
-    cz $2, q[1];
-    c = measure $2;
+    {operation}
     """
-    expected_qasm = """OPENQASM 3.0;
-    qubit[5] __PYQASM_QUBITS__;
+    result = loads(qasm, device_qubits=5)
+    with pytest.raises(
+        ValidationError, match=r"mixes declared registers with physical qubits \(\$2\)"
+    ):
+        result.unroll(consolidate_qubits=True)
+
+
+def test_zero_sized_register_still_counts_as_declared():
+    """A zero-sized declared register is still a second address space (Argus P1)."""
+    qasm = """OPENQASM 3.0;
     include "stdgates.inc";
-    bit[1] c;
-    h __PYQASM_QUBITS__[0];
-    cz $2, __PYQASM_QUBITS__[1];
-    c = measure $2;
+    qubit[0] q;
+    h $1;
+    """
+    result = loads(qasm)
+    with pytest.raises(ValidationError, match=r"mixes declared registers with physical qubits"):
+        result.unroll(consolidate_qubits=True)
+
+
+def test_mixed_declared_and_physical_still_unrolls_without_consolidation():
+    """The mixed-program rejection applies only under consolidate_qubits=True."""
+    qasm = """OPENQASM 3.0;
+    include "stdgates.inc";
+    qubit[2] q;
+    h q[0];
+    cz $2, q[1];
     """
     result = loads(qasm, device_qubits=5)
-    result.unroll(consolidate_qubits=True)
-    check_unrolled_qasm(dumps(result), expected_qasm)
-    # two consolidated slots plus physical $2, which sizes the count to its own index + 1.
-    # neither number is the declared qubit[5], which comes from device_qubits (see #353)
+    result.unroll()
     assert result.num_qubits == 3
 
 
 def test_physical_qubits_only():
+    """With nothing to consolidate, no internal register is declared: the program
+    keeps speaking the physical address space alone (issue #353)."""
     qasm = """OPENQASM 3.0;
     include "stdgates.inc";
     h $1;
     cz $2, $1;
     """
     expected_qasm = """OPENQASM 3.0;
-    qubit[5] __PYQASM_QUBITS__;
     include "stdgates.inc";
     h $1;
     cz $2, $1;
@@ -373,6 +398,17 @@ def test_physical_qubits_only():
     result = loads(qasm, device_qubits=5)
     result.unroll(consolidate_qubits=True)
     check_unrolled_qasm(dumps(result), expected_qasm)
-    # nothing was consolidated, so the count comes entirely from the physical indices
-    # while the emitted declaration is sized by device_qubits (see #353)
+    # the count comes entirely from the physical indices
     assert result.num_qubits == 3
+
+
+def test_physical_qubits_only_without_device_qubits():
+    """The unreferenced declaration is suppressed with or without device_qubits set."""
+    qasm = """OPENQASM 3.0;
+    include "stdgates.inc";
+    h $1;
+    """
+    result = loads(qasm)
+    result.unroll(consolidate_qubits=True)
+    assert "__PYQASM_QUBITS__" not in dumps(result)
+    assert result.num_qubits == 2