diff --git a/package/CHANGELOG b/package/CHANGELOG
index ef0a8c5a631..d262424c8c5 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -27,6 +27,8 @@ Changes
   * Maximum pinned versions in setup.py removed for python 3.6+ (PR #3139)
 
 Deprecations
+  * Deprecated tempfactors and bfactors being separate
+    TopologyAttrs, with a warning (PR #3161)
   * hbonds.WaterBridgeAnalysis will be removed in 2.0.0 and
     replaced with hydrogenbonds.WaterBridgeAnalysis (#3111)
     
diff --git a/package/MDAnalysis/core/universe.py b/package/MDAnalysis/core/universe.py
index 2ae4343247b..4f1f39cf0f2 100644
--- a/package/MDAnalysis/core/universe.py
+++ b/package/MDAnalysis/core/universe.py
@@ -830,6 +830,14 @@ def add_TopologyAttr(self, topologyattr, values=None):
            Can now also add TopologyAttrs with a string of the name of the
            attribute to add (eg 'charges'), can also supply initial values
            using values keyword.
+
+        .. versionchanged:: 1.1.0 
+            Now warns when adding bfactors to a Universe with
+            existing tempfactors, or adding tempfactors to a
+            Universe with existing bfactors.
+            In version 2.0, MDAnalysis will stop treating
+            tempfactors and bfactors as separate attributes. Instead,
+            they will be aliases of the same attribute.
         """
         if isinstance(topologyattr, six.string_types):
             try:
@@ -850,6 +858,16 @@ def add_TopologyAttr(self, topologyattr, values=None):
                     n_residues=self._topology.n_residues,
                     n_segments=self._topology.n_segments,
                     values=values)
+        alias_pairs = [("bfactors", "tempfactors"),
+                       ("tempfactors", "bfactors")]
+        for a, b in alias_pairs:
+            if topologyattr.attrname == a and hasattr(self._topology, b):
+                err = ("You are adding {a} to a Universe that "
+                       "has {b}. From MDAnalysis version 2.0, {a} "
+                       "and {b} will no longer be separate "
+                       "TopologyAttrs. Instead, they will be aliases "
+                       "of the same attribute.").format(a=a, b=b)
+                warnings.warn(err, DeprecationWarning)
         self._topology.add_TopologyAttr(topologyattr)
         self._process_attr(topologyattr)
 
diff --git a/testsuite/MDAnalysisTests/core/test_universe.py b/testsuite/MDAnalysisTests/core/test_universe.py
index 7eb5c091a57..3dd7f5cc1f6 100644
--- a/testsuite/MDAnalysisTests/core/test_universe.py
+++ b/testsuite/MDAnalysisTests/core/test_universe.py
@@ -51,6 +51,7 @@
     GRO, TRR,
     two_water_gro, two_water_gro_nonames,
     TRZ, TRZ_psf,
+    PDB, MMTF,
 )
 
 import MDAnalysis as mda
@@ -1136,3 +1137,15 @@ def test_empty_creation_raises_error(self):
 def test_as_Universe_deprecation():
     with pytest.deprecated_call():
         _ = mda.core.universe.as_Universe(PSF, DCD)
+
+
+def test_deprecate_b_tempfactors():
+    u = mda.Universe(PDB)
+    with pytest.warns(DeprecationWarning, match="alias"):
+        u.add_TopologyAttr("bfactors")
+
+
+def test_deprecate_temp_bfactors():
+    u = mda.Universe(MMTF)
+    with pytest.warns(DeprecationWarning, match="alias"):
+        u.add_TopologyAttr("tempfactors")