diff --git a/pySC/configuration/bpm_system_conf.py b/pySC/configuration/bpm_system_conf.py
index bc547172..f9a5452e 100644
--- a/pySC/configuration/bpm_system_conf.py
+++ b/pySC/configuration/bpm_system_conf.py
@@ -2,7 +2,6 @@
 import logging
 
 from ..core.simulated_commissioning import SimulatedCommissioning
-from ..core.bpm_system import BPM_FIELDS_TO_INITIALISE, BPM_FIELDS_TO_INITIALISE_ONES
 from .general import get_error, get_indices_and_names
 from .supports_conf import generate_element_misalignments
 
@@ -87,11 +86,7 @@ def configure_bpms(SC: SimulatedCommissioning) -> None:
     SC.bpm_system.noise_tbt_x = np.array(bpms_tbt_noise)
     SC.bpm_system.noise_tbt_y = np.array(bpms_tbt_noise)
 
-    nbpm = len(bpms_indices)
-    for field in BPM_FIELDS_TO_INITIALISE:
-        setattr(SC.bpm_system, field, np.zeros(nbpm, dtype=float))
-    for field in BPM_FIELDS_TO_INITIALISE_ONES:
-        setattr(SC.bpm_system, field, np.ones(nbpm, dtype=float))
+    SC.bpm_system.initialize_empty_arrays()
 
     for index, bpm_category in zip(bpms_indices, bpms_categories):
         generate_element_misalignments(SC, index, bpms_conf[bpm_category])
diff --git a/pySC/core/bpm_system.py b/pySC/core/bpm_system.py
index 281c58cb..6d8e80ce 100644
--- a/pySC/core/bpm_system.py
+++ b/pySC/core/bpm_system.py
@@ -12,9 +12,9 @@
 def _rotation_matrix(a):
     return np.array([[np.cos(a), -np.sin(a)], [np.sin(a), np.cos(a)]])
 
-BPM_FIELDS_TO_INITIALISE = ['offsets_x', 'offsets_y', 'rolls',
-                            'bba_offsets_x', 'bba_offsets_y',
-                            'reference_x', 'reference_y']
+BPM_FIELDS_TO_INITIALISE_ZEROS = ['offsets_x', 'offsets_y', 'rolls',
+                                  'bba_offsets_x', 'bba_offsets_y',
+                                  'reference_x', 'reference_y']
 
 # These fields are initialized to ones (not zeros) — multiplicative corrections
 BPM_FIELDS_TO_INITIALISE_ONES = ['gain_corrections_x', 'gain_corrections_y']
@@ -54,8 +54,19 @@ class BPMSystem(BaseModel, extra='forbid'):
     def initialize(self):
         if len(self.rolls) > 0:
             self.update_rot_matrices()
+        if len(self.indices):
+            self.initialize_empty_arrays()
         return self
 
+    def initialize_empty_arrays(self):
+        nbpm = len(self.indices)
+        for field in BPM_FIELDS_TO_INITIALISE_ZEROS:
+            if not len(getattr(self, field)): # array is empty
+                setattr(self, field, np.zeros(nbpm, dtype=float))
+        for field in BPM_FIELDS_TO_INITIALISE_ONES:
+            if not len(getattr(self, field)): # array is empty
+                setattr(self, field, np.ones(nbpm, dtype=float))
+
     def update_rot_matrices(self):
         self._rot_matrices = _rotation_matrix(self.rolls)
 
diff --git a/tests/core/test_bpm_system.py b/tests/core/test_bpm_system.py
index c6013bfc..7f9d3984 100644
--- a/tests/core/test_bpm_system.py
+++ b/tests/core/test_bpm_system.py
@@ -69,6 +69,56 @@ def test_gain_corrections_default_ones(sc):
     np.testing.assert_array_equal(bpm.gain_corrections_y, np.ones(len(bpm.indices)))
 
 
+# ---------------------------------------------------------------------------
+# backwards-compatible field initialisation
+# ---------------------------------------------------------------------------
+
+def test_bpm_system_initializes_missing_empty_arrays():
+    """Older payloads with BPM indices get missing BPM arrays initialized."""
+    bpm = BPMSystem(
+        indices=[10, 20, 30],
+        names=['BPM1', 'BPM2', 'BPM3'],
+        calibration_errors_x=[0.0, 0.0, 0.0],
+        calibration_errors_y=[0.0, 0.0, 0.0],
+        noise_co_x=[0.0, 0.0, 0.0],
+        noise_co_y=[0.0, 0.0, 0.0],
+        noise_tbt_x=[0.0, 0.0, 0.0],
+        noise_tbt_y=[0.0, 0.0, 0.0],
+    )
+
+    for field in ['offsets_x', 'offsets_y', 'rolls', 'bba_offsets_x', 'bba_offsets_y',
+                  'reference_x', 'reference_y']:
+        np.testing.assert_array_equal(getattr(bpm, field), np.zeros(3), err_msg=field)
+
+    np.testing.assert_array_equal(bpm.gain_corrections_x, np.ones(3))
+    np.testing.assert_array_equal(bpm.gain_corrections_y, np.ones(3))
+
+
+def test_bpm_system_initialize_empty_arrays_preserves_existing_values():
+    """initialize_empty_arrays fills only empty fields and preserves supplied arrays."""
+    bpm = BPMSystem(
+        indices=[10, 20],
+        offsets_x=[1.0, 2.0],
+        gain_corrections_x=[3.0, 4.0],
+    )
+
+    bpm.initialize_empty_arrays()
+
+    np.testing.assert_array_equal(bpm.offsets_x, np.array([1.0, 2.0]))
+    np.testing.assert_array_equal(bpm.gain_corrections_x, np.array([3.0, 4.0]))
+    np.testing.assert_array_equal(bpm.offsets_y, np.zeros(2))
+    np.testing.assert_array_equal(bpm.gain_corrections_y, np.ones(2))
+
+
+def test_bpm_system_validation_updates_rot_matrices_when_rolls_provided():
+    """Validation still builds rotation matrices when rolls are present."""
+    bpm = BPMSystem(indices=[10, 20], rolls=[0.0, 0.1])
+
+    assert bpm._rot_matrices is not None
+    assert bpm._rot_matrices.shape == (2, 2, 2)
+    np.testing.assert_array_almost_equal(bpm._rot_matrices[:, :, 0], np.eye(2))
+
+
 # ---------------------------------------------------------------------------
 # einsum rotation contraction
 # ---------------------------------------------------------------------------