diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
index afb6c2602..390e4daf0 100644
--- a/fmriprep/workflows/base.py
+++ b/fmriprep/workflows/base.py
@@ -302,6 +302,8 @@ def init_single_subject_wf(subject_id):
 
     for bold_file in subject_data['bold']:
         func_preproc_wf = init_func_preproc_wf(bold_file)
+        if func_preproc_wf is None:
+            continue
 
         try:
             workflow.connect([
diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index e5161c791..fbbeabae7 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -144,6 +144,12 @@ def init_func_preproc_wf(bold_file):
     from niworkflows.interfaces.utils import DictMerge
     from sdcflows.workflows.base import init_sdc_estimate_wf, fieldmap_wrangler
 
+    if nb.load(bold_file).shape[3:] <= (5,):
+        config.loggers.workflow.warning(
+            f"Too short BOLD series  (<= 5 timepoints). Skipping processing of <{ref_file}>."
+        )
+        return
+
     mem_gb = {'filesize': 1, 'resampled': 1, 'largemem': 1}
     bold_tlen = 10