diff --git a/.coveragerc b/.coveragerc
index f87af87aa8..b7e90a3600 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -1,7 +1,9 @@
 [run]
 branch = True
 source = MDAnalysis
-plugins = Cython.Coverage
+# Cython.Coverage plugin disabled for Cython >= 3.1.0 compatibility (Issue #5057).
+# Cython 3.1+ has worker crash bugs with linetrace which is required by the
+# Cython.Coverage plugin, so we disable the plugin to prevent test crashes.
 omit =
     */MDAnalysis/tests/*
     */legacy/*
diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml
index 76f3b518f3..654d86d43a 100644
--- a/.github/workflows/gh-ci-cron.yaml
+++ b/.github/workflows/gh-ci-cron.yaml
@@ -295,7 +295,7 @@ jobs:
     - name: install_deps
       shell: bash
       run: |
-          pip install pytest-xdist pytest-timeout "numpy<2.3" "cython<3.1" wheel "setuptools>=40.9.0" packaging
+          pip install pytest-xdist pytest-timeout "numpy<2.3" cython wheel "setuptools>=40.9.0" packaging
 
     - name: install_mdanalysis
       shell: bash
diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml
index 99894ca434..0011bb3093 100644
--- a/.github/workflows/gh-ci.yaml
+++ b/.github/workflows/gh-ci.yaml
@@ -31,36 +31,27 @@ jobs:
           python-version: ["3.11", "3.12", "3.13"]
           full-deps: [true, ]
           codecov: [true, ]
-          cython: ["cython<3.1", ]
           include:
-            # Including 3.14 and 3.11 without coverage
-            # and cython >=3.1 to deal temporarily with
-            # keeping on testing Cython whilst issue #5057
-            # is not fixed
             - name: python_314_nocov
               os: ubuntu-latest
               python-version: "3.14"
               full-deps: false
               codecov: false
-              cython: "cython>=3.1"
             - name: python_311_nocov
               os: ubuntu-latest
               python-version: "3.11"
               full-deps: false
               codecov: false
-              cython: "cython>=3.1"
             - name: macOS_14_arm64_py313
               os: macOS-14
               python-version: "3.13"
               full-deps: false
               codecov: true
-              cython: "cython<3.1"
             - name: ubuntu_arm
               os: ubuntu-24.04-arm
               python-version: "3.13"
               full-deps: false
               codecov: false
-              cython: "cython>3.1"
             - name: numpy_min
               os: ubuntu-latest
               python-version: "3.11"
@@ -105,7 +96,6 @@ jobs:
         full-deps: ${{ matrix.full-deps }}
         # disable GSD because it occasionally introduce hanging in testing #4209
         gsd: ''
-        # pin cython
         cython: ${{ matrix.cython }}
         # in most cases will just default to empty, i.e. pick up max version from other deps
         numpy: ${{ matrix.numpy }}
diff --git a/package/AUTHORS b/package/AUTHORS
index c8ba87c062..dba8be1110 100644
--- a/package/AUTHORS
+++ b/package/AUTHORS
@@ -285,6 +285,7 @@ Chronological list of authors
   - Apoorva Verma
   - Aryaman Chaudhri
   - Francesco Siciliani
+  - Akshit Boora
 
 External code
 -------------
diff --git a/package/CHANGELOG b/package/CHANGELOG
index 45647f3904..8911a9d685 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -18,11 +18,13 @@ The rules for this file:
          spyke7, talagayev, tanii1125, BradyAJohnston, hejamu, jeremyleung521,
          harshitgajjela-droid, kunjsinha, aygarwal, jauy123, Dreamstick9,
          ollyfutur, Amarendra22, charity-g, ParthUppal523, apoorva-01, RMeli,
-         raulloiscuns, Aryaman-Chaudhri, sici17
+         raulloiscuns, Aryaman-Chaudhri, sici17, AkshitBoora
 
  * 2.11.0
 
 Fixes
+ * Unpinned Cython version constraint and restored support for Cython >= 3.1.0
+   (Issue #5057)
  * Mass (u) has been added to MDAnalysis base units and clarified that physical
    constants use CODATA 2010 values (Issue #3944, PR #5439)
  * Added `.gitattributes` to enforce LF (\n) as line endings and renormalized
diff --git a/package/setup.py b/package/setup.py
index f9b7b4a9e7..6beab963f1 100755
--- a/package/setup.py
+++ b/package/setup.py
@@ -83,7 +83,11 @@
             )
         )
         cython_found = False
-    cython_linetrace = bool(os.environ.get("CYTHON_TRACE_NOGIL", False))
+    if Version(Cython.__version__) >= Version("3.1.0"):
+        # Cython 3.1+ has worker crash bugs with linetrace (Issue #5057)
+        cython_linetrace = False
+    else:
+        cython_linetrace = bool(os.environ.get("CYTHON_TRACE_NOGIL", False))
 except ImportError:
     cython_found = False
     if not is_release:
@@ -353,8 +357,15 @@ def extensions(config):
         mathlib = ["m"]
 
     if cython_linetrace:
-        extra_compile_args.append("-DCYTHON_TRACE_NOGIL")
-        cpp_extra_compile_args.append("-DCYTHON_TRACE_NOGIL")
+        extra_compile_args.extend(
+            ["-DCYTHON_TRACE_NOGIL=1", "-DCYTHON_TRACE=1"]
+        )
+        cpp_extra_compile_args.extend(
+            ["-DCYTHON_TRACE_NOGIL=1", "-DCYTHON_TRACE=1"]
+        )
+        encore_compile_args.extend(
+            ["-DCYTHON_TRACE_NOGIL=1", "-DCYTHON_TRACE=1"]
+        )
 
     libdcd = MDAExtension(
         "MDAnalysis.lib.formats.libdcd",