diff --git a/package/CHANGELOG b/package/CHANGELOG
index de7fddd2660..7fa3a3501a2 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -99,6 +99,8 @@ Changes
    numpy.testing.assert_allclose #4438)
 
 Deprecations
+ * The MDAnalysis.anaylsis.encore module has been deprecated in favour of the
+   mdaencore MDAKit and will be removed in version 3.0.0 (PR #4737)
  * The MMTF Reader is deprecated and will be removed in version 3.0
    as the MMTF format is no longer supported (Issue #4634)
  * The MDAnalysis.analysis.waterdynamics module has been deprecated in favour
diff --git a/package/MDAnalysis/analysis/encore/__init__.py b/package/MDAnalysis/analysis/encore/__init__.py
index 2017188580f..34b70dd28d0 100644
--- a/package/MDAnalysis/analysis/encore/__init__.py
+++ b/package/MDAnalysis/analysis/encore/__init__.py
@@ -34,6 +34,14 @@
 
 __all__ = ['covariance', 'similarity', 'confdistmatrix', 'clustering']
 
+import warnings
+
+wmsg = ("Deprecation in version 2.8.0\n"
+        "MDAnalysis.analysis.encore is deprecated in favour of the "
+        "MDAKit mdaencore (https://www.mdanalysis.org/mdaencore/) "
+        "and will be removed in MDAnalysis version 3.0.0.")
+warnings.warn(wmsg, category=DeprecationWarning)
+
 from ...due import due, Doi
 
 due.cite(Doi("10.1371/journal.pcbi.1004415"),
diff --git a/package/MDAnalysis/analysis/encore/bootstrap.py b/package/MDAnalysis/analysis/encore/bootstrap.py
index 22287d98fc7..2d50d486dcb 100644
--- a/package/MDAnalysis/analysis/encore/bootstrap.py
+++ b/package/MDAnalysis/analysis/encore/bootstrap.py
@@ -32,6 +32,11 @@
 
 .. versionadded:: 0.16.0
 
+.. deprecated:: 2.8.0
+   This module is deprecated in favour of the 
+   MDAKit `mdaencore <https://mdanalysis.org/mdaencore/>`_ and will be removed
+   in MDAnalysis 3.0.0.
+
 """
 import numpy as np
 import logging
diff --git a/package/MDAnalysis/analysis/encore/clustering/ClusterCollection.py b/package/MDAnalysis/analysis/encore/clustering/ClusterCollection.py
index 35b48219abf..87879ba1077 100644
--- a/package/MDAnalysis/analysis/encore/clustering/ClusterCollection.py
+++ b/package/MDAnalysis/analysis/encore/clustering/ClusterCollection.py
@@ -31,6 +31,11 @@
 
 .. versionadded:: 0.16.0
 
+.. deprecated:: 2.8.0
+   This module is deprecated in favour of the 
+   MDAKit `mdaencore <https://mdanalysis.org/mdaencore/>`_ and will be removed
+   in MDAnalysis 3.0.0.
+
 """
 import numpy as np
 
diff --git a/package/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py b/package/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py
index b18d6a54350..df13aaff570 100644
--- a/package/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py
+++ b/package/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py
@@ -32,6 +32,11 @@
 
 .. versionadded:: 0.16.0
 
+.. deprecated:: 2.8.0
+   This module is deprecated in favour of the 
+   MDAKit `mdaencore <https://mdanalysis.org/mdaencore/>`_ and will be removed
+   in MDAnalysis 3.0.0.
+
 """
 import numpy as np
 import warnings
diff --git a/package/MDAnalysis/analysis/encore/clustering/cluster.py b/package/MDAnalysis/analysis/encore/clustering/cluster.py
index 9e0ea01fc45..0ad713775d6 100644
--- a/package/MDAnalysis/analysis/encore/clustering/cluster.py
+++ b/package/MDAnalysis/analysis/encore/clustering/cluster.py
@@ -31,6 +31,11 @@
 
 .. versionadded:: 0.16.0
 
+.. deprecated:: 2.8.0
+   This module is deprecated in favour of the 
+   MDAKit `mdaencore <https://mdanalysis.org/mdaencore/>`_ and will be removed
+   in MDAnalysis 3.0.0.
+
 """
 import numpy as np
 from ..utils import ParallelCalculation, merge_universes
diff --git a/package/MDAnalysis/analysis/encore/confdistmatrix.py b/package/MDAnalysis/analysis/encore/confdistmatrix.py
index 483964d5594..2f3e83b94ff 100644
--- a/package/MDAnalysis/analysis/encore/confdistmatrix.py
+++ b/package/MDAnalysis/analysis/encore/confdistmatrix.py
@@ -34,6 +34,11 @@ class to compute an RMSD matrix in such a way is also available.
 
 .. versionadded:: 0.16.0
 
+.. deprecated:: 2.8.0
+   This module is deprecated in favour of the 
+   MDAKit `mdaencore <https://mdanalysis.org/mdaencore/>`_ and will be removed
+   in MDAnalysis 3.0.0.
+
 """
 from joblib import Parallel, delayed
 import numpy as np
diff --git a/package/MDAnalysis/analysis/encore/covariance.py b/package/MDAnalysis/analysis/encore/covariance.py
index 1fb77b10785..e6768bf698d 100644
--- a/package/MDAnalysis/analysis/encore/covariance.py
+++ b/package/MDAnalysis/analysis/encore/covariance.py
@@ -30,6 +30,12 @@
 :Author: Matteo Tiberti, Wouter Boomsma, Tone Bengtsen
 
 .. versionadded:: 0.16.0
+
+.. deprecated:: 2.8.0
+   This module is deprecated in favour of the 
+   MDAKit `mdaencore <https://mdanalysis.org/mdaencore/>`_ and will be removed
+   in MDAnalysis 3.0.0.
+
 """
 import numpy as np
 
diff --git a/package/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py b/package/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py
index 10cd28ce4d6..cef202843d7 100644
--- a/package/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py
+++ b/package/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py
@@ -32,6 +32,11 @@
 
 .. versionadded:: 0.16.0
 
+.. deprecated:: 2.8.0
+   This module is deprecated in favour of the 
+   MDAKit `mdaencore <https://mdanalysis.org/mdaencore/>`_ and will be removed
+   in MDAnalysis 3.0.0.
+
 """
 import logging
 import warnings
diff --git a/package/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py b/package/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py
index 1432c4a06de..1a35548fbf6 100644
--- a/package/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py
+++ b/package/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py
@@ -31,6 +31,11 @@
 
 .. versionadded:: 0.16.0
 
+.. deprecated:: 2.8.0
+   This module is deprecated in favour of the 
+   MDAKit `mdaencore <https://mdanalysis.org/mdaencore/>`_ and will be removed
+   in MDAnalysis 3.0.0.
+
 """
 import numpy as np
 from ..confdistmatrix import get_distance_matrix
diff --git a/package/MDAnalysis/analysis/encore/similarity.py b/package/MDAnalysis/analysis/encore/similarity.py
index 9e1ee2a6749..2f41d233d48 100644
--- a/package/MDAnalysis/analysis/encore/similarity.py
+++ b/package/MDAnalysis/analysis/encore/similarity.py
@@ -29,6 +29,11 @@
 
 .. versionadded:: 0.16.0
 
+.. deprecated:: 2.8.0
+   This module is deprecated in favour of the 
+   MDAKit `mdaencore <https://mdanalysis.org/mdaencore/>`_ and will be removed
+   in MDAnalysis 3.0.0.
+
 The module contains implementations of similarity measures between protein
 ensembles described in :footcite:p:`LindorffLarsen2009`. The implementation and
 examples are described in :footcite:p:`Tiberti2015`.
diff --git a/package/doc/sphinx/source/documentation_pages/analysis/encore.rst b/package/doc/sphinx/source/documentation_pages/analysis/encore.rst
index 2051a2e3352..d4da4612601 100644
--- a/package/doc/sphinx/source/documentation_pages/analysis/encore.rst
+++ b/package/doc/sphinx/source/documentation_pages/analysis/encore.rst
@@ -9,6 +9,12 @@
 
 .. versionadded:: 0.16.0
 
+
+.. deprecated:: 2.8.0
+   This module is deprecated in favour of the 
+   MDAKit `mdaencore <https://mdanalysis.org/mdaencore/>`_ and will be removed
+   in MDAnalysis 3.0.0.
+
 The module contains implementations of similarity measures between protein
 ensembles described in :footcite:p:`LindorffLarsen2009`. The implementation and examples
 are described in :footcite:p:`Tiberti2015`.
diff --git a/package/doc/sphinx/source/documentation_pages/analysis/encore/utils.rst b/package/doc/sphinx/source/documentation_pages/analysis/encore/utils.rst
index 85a2f6cd414..e1b1e27b717 100644
--- a/package/doc/sphinx/source/documentation_pages/analysis/encore/utils.rst
+++ b/package/doc/sphinx/source/documentation_pages/analysis/encore/utils.rst
@@ -2,6 +2,11 @@
  Utility functions for ENCORE
 ==============================
 
+.. deprecated:: 2.8.0
+   This module is deprecated in favour of the 
+   MDAKit `mdaencore <https://mdanalysis.org/mdaencore/>`_ and will be removed
+   in MDAnalysis 3.0.0.
+
 .. automodule:: MDAnalysis.analysis.encore.utils
    :members:
 
diff --git a/testsuite/MDAnalysisTests/analysis/test_encore.py b/testsuite/MDAnalysisTests/analysis/test_encore.py
index bc07c21af73..424aae54278 100644
--- a/testsuite/MDAnalysisTests/analysis/test_encore.py
+++ b/testsuite/MDAnalysisTests/analysis/test_encore.py
@@ -30,6 +30,7 @@
 import os
 import warnings
 import platform
+from importlib import reload
 
 import pytest
 from numpy.testing import assert_equal, assert_allclose
@@ -46,6 +47,11 @@ def function(x):
     return x**2
 
 
+def test_moved_to_mdakit_warning():
+    wmsg = "MDAnalysis.analysis.encore is deprecated"
+    with pytest.warns(DeprecationWarning, match=wmsg):
+        reload(encore)
+
 class TestEncore(object):
     @pytest.fixture(scope='class')
     def ens1_template(self):