diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
index a27a04157..44368f1d4 100644
--- a/fmriprep/workflows/base.py
+++ b/fmriprep/workflows/base.py
@@ -429,10 +429,20 @@ def init_single_subject_wf(subject_id: str):
 
             fmap_estimators = [fmap for fmap in fmap_estimators if fmap.bids_id in used_estimators]
 
+            # Simplification: Unused estimators are removed from registry
+            # This fiddles with a private attribute, so it may break in future
+            # versions. However, it does mean the BOLD workflow doesn't need to
+            # replicate the logic that got us to the pared down set of estimators
+            # here.
+            final_ids = {fmap.bids_id for fmap in fmap_estimators}
+            unused_ids = fm._estimators.keys() - final_ids
+            for bids_id in unused_ids:
+                del fm._estimators[bids_id]
+
         if fmap_estimators:
             config.loggers.workflow.info(
                 "B0 field inhomogeneity map will be estimated with "
-                f" the following {len(fmap_estimators)} estimators: "
+                f"the following {len(fmap_estimators)} estimator(s): "
                 f"{[e.method for e in fmap_estimators]}."
             )
 
@@ -563,8 +573,8 @@ def init_single_subject_wf(subject_id: str):
         elif estimator.method == fm.EstimatorType.ANAT:
             from sdcflows.workflows.fit.syn import init_syn_preprocessing_wf
 
-            sources = [str(s.path) for s in estimator.sources if s.suffix == "bold"]
-            source_meta = [s.metadata for s in estimator.sources if s.suffix == "bold"]
+            sources = [str(s.path) for s in estimator.sources if s.suffix in ("bold", "sbref")]
+            source_meta = [s.metadata for s in estimator.sources if s.suffix in ("bold", "sbref")]
             syn_preprocessing_wf = init_syn_preprocessing_wf(
                 omp_nthreads=config.nipype.omp_nthreads,
                 debug=config.execution.sloppy,
diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index ab6cdc1ee..aabe49c9e 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -289,7 +289,14 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
     config.loggers.workflow.info(sbref_msg)
 
     if has_fieldmap:
-        estimator_key = get_estimator(layout, bold_file if not multiecho else bold_file[0])
+        from sdcflows import fieldmaps as fm
+
+        # We may have pruned the estimator collection due to `--ignore fieldmaps`
+        estimator_key = [
+            key
+            for key in get_estimator(layout, bold_file if not multiecho else bold_file[0])
+            if key in fm._estimators
+        ]
 
         if not estimator_key:
             has_fieldmap = False