diff --git a/sdcflows/interfaces/bspline.py b/sdcflows/interfaces/bspline.py
index ccb9ad3c7f..6292a4199d 100644
--- a/sdcflows/interfaces/bspline.py
+++ b/sdcflows/interfaces/bspline.py
@@ -327,7 +327,18 @@ class _TOPUPCoeffReorientInputSpec(BaseInterfaceInputSpec):
         File(exist=True), mandatory=True, desc="input coefficients file(s) from TOPUP"
     )
     fmap_ref = File(exists=True, mandatory=True, desc="the fieldmap reference")
-
+    pe_dir = traits.Enum(
+        "+",
+        "-",
+        "i",
+        "i-",
+        "j",
+        "j-",
+        "k",
+        "k-",
+        usedefault=True,
+        desc="the polarity of the phase-encoding direction corresponding to fmap_ref",
+    )
 
 class _TOPUPCoeffReorientOutputSpec(TraitedSpec):
     out_coeff = OutputMultiObject(File(exists=True), desc="patched coefficients")
@@ -368,7 +379,8 @@ def _run_interface(self, runtime):
                 _fix_topup_fieldcoeff(
                     in_coeff,
                     self.inputs.fmap_ref,
-                    fname_presuffix(in_coeff, suffix="_fixed", newpath=runtime.cwd),
+                    refpe_reversed=self.inputs.pe_dir.endswith("-"),
+                    out_file=fname_presuffix(in_coeff, suffix="_fixed", newpath=runtime.cwd),
                 )
             )
             for in_coeff in self.inputs.in_coeff
@@ -598,7 +610,7 @@ def _move_coeff(in_coeff, fmap_ref, transform):
     return out
 
 
-def _fix_topup_fieldcoeff(in_coeff, fmap_ref, out_file=None):
+def _fix_topup_fieldcoeff(in_coeff, fmap_ref, refpe_reversed=False, out_file=None):
     """Read in a coefficients file generated by TOPUP and fix x-form headers."""
     from pathlib import Path
     import numpy as np
@@ -627,5 +639,7 @@ def _fix_topup_fieldcoeff(in_coeff, fmap_ref, out_file=None):
     coeffnii.header.set_qform(coeffnii.header.get_qform(coded=False), code=0)
     coeffnii.header.set_sform(newaff, code=1)
 
-    coeffnii.__class__(coeffnii.dataobj, newaff, header).to_filename(out_file)
+    # If the reference is reversed encoded, flip the displacements
+    coeffs = (1.0 - 2.0 * refpe_reversed) * np.asanyarray(coeffnii.dataobj)
+    coeffnii.__class__(coeffs, newaff, header).to_filename(out_file)
     return out_file
diff --git a/sdcflows/workflows/fit/pepolar.py b/sdcflows/workflows/fit/pepolar.py
index b78fd49283..c0ea10eda2 100644
--- a/sdcflows/workflows/fit/pepolar.py
+++ b/sdcflows/workflows/fit/pepolar.py
@@ -72,6 +72,7 @@ def init_topup_wf(omp_nthreads=1, sloppy=False, debug=False, name="pepolar_estim
     from niworkflows.interfaces.nibabel import MergeSeries
     from niworkflows.interfaces.images import IntraModalMerge
 
+    from ...utils.misc import front as _front
     from ...interfaces.epi import GetReadoutTime
     from ...interfaces.utils import Flatten
     from ...interfaces.bspline import TOPUPCoeffReorient
@@ -125,6 +126,11 @@ def init_topup_wf(omp_nthreads=1, sloppy=False, debug=False, name="pepolar_estim
 
     brainextraction_wf = init_brainextraction_wf()
 
+    def _getpe(in_meta):
+        if isinstance(in_meta, list):
+            in_meta = in_meta[0]
+        return in_meta["PhaseEncodingDirection"]
+
     # fmt: off
     workflow.connect([
         (inputnode, flatten, [("in_data", "in_data"),
@@ -135,9 +141,10 @@ def init_topup_wf(omp_nthreads=1, sloppy=False, debug=False, name="pepolar_estim
         (flatten, topup, [(("out_meta", _pe2fsl), "encoding_direction")]),
         (readout_time, topup, [("readout_time", "readout_times")]),
         (concat_blips, topup, [("out_file", "in_file")]),
+        (flatten, fix_coeff, [(("out_data", _front), "fmap_ref"),
+                              (("out_meta", _getpe), "pe_dir")]),
+        (topup, fix_coeff, [("out_fieldcoef", "in_coeff")]),
         (topup, merge_corrected, [("out_corrected", "in_files")]),
-        (topup, fix_coeff, [("out_fieldcoef", "in_coeff"),
-                            ("out_corrected", "fmap_ref")]),
         (topup, outputnode, [("out_field", "fmap"),
                              ("out_jacs", "jacobians"),
                              ("out_mats", "xfms"),