diff --git a/crates/accelerate/src/sabre_swap/mod.rs b/crates/accelerate/src/sabre_swap/mod.rs
index 12c21cbd1ce1..8549d7001cc3 100644
--- a/crates/accelerate/src/sabre_swap/mod.rs
+++ b/crates/accelerate/src/sabre_swap/mod.rs
@@ -415,8 +415,8 @@ fn swap_map_trial(
                 qubits_decay.fill(1.);
                 num_search_steps = 0;
             } else {
-                qubits_decay[best_swap[0]] += DECAY_RATE;
-                qubits_decay[best_swap[1]] += DECAY_RATE;
+                qubits_decay[layout.logic_to_phys[best_swap[0]]] += DECAY_RATE;
+                qubits_decay[layout.logic_to_phys[best_swap[1]]] += DECAY_RATE;
             }
         }
         // If we exceeded the number of allowed attempts without successfully routing a node, we
@@ -735,7 +735,8 @@ fn choose_best_swap(
                     + EXTENDED_SET_WEIGHT * extended_set.score(swap, layout, dist)
             }
             Heuristic::Decay => {
-                qubits_decay[swap[0]].max(qubits_decay[swap[1]])
+                qubits_decay[layout.logic_to_phys[swap[0]]]
+                    .max(qubits_decay[layout.logic_to_phys[swap[1]]])
                     * (absolute_score
                         + layer.score(swap, layout, dist)
                         + EXTENDED_SET_WEIGHT * extended_set.score(swap, layout, dist))
diff --git a/releasenotes/notes/sabre-decay-physical-ad2f470cd45d69f3.yaml b/releasenotes/notes/sabre-decay-physical-ad2f470cd45d69f3.yaml
new file mode 100644
index 000000000000..8d647d5b13d5
--- /dev/null
+++ b/releasenotes/notes/sabre-decay-physical-ad2f470cd45d69f3.yaml
@@ -0,0 +1,6 @@
+---
+fixes:
+  - |
+    The ``"decay"`` heuristic of :class:`.SabreSwap` and :class:`.SabreLayout` now tracks the depth
+    correctly on physical qubits rather than mistakenly tracking the "depth" of swaps on virtual
+    qubits.
diff --git a/test/python/transpiler/test_sabre_layout.py b/test/python/transpiler/test_sabre_layout.py
index 2c41de46df04..ff9788521c16 100644
--- a/test/python/transpiler/test_sabre_layout.py
+++ b/test/python/transpiler/test_sabre_layout.py
@@ -60,7 +60,7 @@ def test_5q_circuit_20q_coupling(self):
         pass_.run(dag)
 
         layout = pass_.property_set["layout"]
-        self.assertEqual([layout[q] for q in circuit.qubits], [11, 10, 16, 5, 17])
+        self.assertEqual([layout[q] for q in circuit.qubits], [16, 7, 11, 12, 13])
 
     def test_6q_circuit_20q_coupling(self):
         """Test finds layout for 6q circuit on 20q device."""