diff --git a/package/MDAnalysis/analysis/encore/confdistmatrix.py b/package/MDAnalysis/analysis/encore/confdistmatrix.py
index 483964d5594..20fe8ea7e0a 100644
--- a/package/MDAnalysis/analysis/encore/confdistmatrix.py
+++ b/package/MDAnalysis/analysis/encore/confdistmatrix.py
@@ -171,14 +171,25 @@ def conformational_distance_matrix(ensemble,
     # Initialize workers. Simple worker doesn't perform fitting,
     # fitter worker does.
     indices = trm_indices((0, 0), (framesn - 1, framesn - 1))
-    Parallel(n_jobs=n_jobs, verbose=verbose, require='sharedmem',
-            max_nbytes=max_nbytes)(delayed(conf_dist_function)(
-        np.int64(element),
-        rmsd_coordinates,
-        distmat,
-        weights,
-        fitting_coordinates,
-        subset_weights) for element in indices)
+    if n_jobs == 1:
+        for element in indices:
+            conf_dist_function(np.int64(element),
+                               rmsd_coordinates,
+                               distmat,
+                               weights,
+                               fitting_coordinates,
+                               subset_weights)
+    else:
+        Parallel(n_jobs=n_jobs,
+                 verbose=verbose,
+                 require='sharedmem',
+                 max_nbytes=max_nbytes)(delayed(conf_dist_function)(
+            np.int64(element),
+            rmsd_coordinates,
+            distmat,
+            weights,
+            fitting_coordinates,
+            subset_weights) for element in indices)
 
 
     # When the workers have finished, return a TriangularMatrix object