diff --git a/sdcflows/workflows/base.py b/sdcflows/workflows/base.py
index 20f7e4e7aa..7c9c609d10 100644
--- a/sdcflows/workflows/base.py
+++ b/sdcflows/workflows/base.py
@@ -87,11 +87,15 @@ def init_fmap_preproc_wf(
 
     workflow = Workflow(name=name)
 
-    out_fields = ("fmap", "fmap_ref", "fmap_coeff", "fmap_mask", "fmap_id", "method")
+    out_fields = ("fmap", "fmap_coeff", "fmap_ref", "fmap_mask", "fmap_id", "method")
     out_merge = {
         f: pe.Node(niu.Merge(len(estimators)), name=f"out_merge_{f}")
         for f in out_fields
     }
+    # Fieldmaps and coefficient files can come in pairs, ensure they are not flattened
+    out_merge["fmap"].inputs.no_flatten = True
+    out_merge["fmap_coeff"].inputs.no_flatten = True
+
     outputnode = pe.Node(niu.IdentityInterface(fields=out_fields), name="outputnode")
 
     workflow.connect(
diff --git a/sdcflows/workflows/tests/test_base.py b/sdcflows/workflows/tests/test_base.py
index f9f48a5440..97bf753ed3 100644
--- a/sdcflows/workflows/tests/test_base.py
+++ b/sdcflows/workflows/tests/test_base.py
@@ -62,5 +62,15 @@ def test_fmap_wf(tmpdir, workdir, outdir, bids_layouts, dataset, subject):
     if workdir:
         wf.base_dir = str(workdir)
 
-    if os.getenv("GITHUB_ACTIONS") != "true":
-        wf.run(plugin="Linear")
+    if os.getenv("GITHUB_ACTIONS") == "true":
+        return
+
+    res = wf.run(plugin="Linear")
+
+    # Regression test for when out_merge_fmap_coeff was flattened and would
+    # have twice as many elements as the other nodes
+    assert all(
+        len(node.result.outputs.out) == len(estimators)
+        for node in res.nodes
+        if node.name.startswith("out_merge_")
+    )