diff --git a/.coveragerc b/.coveragerc
index d9a48b4b..a72fd709 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -1,2 +1,2 @@
 [run]
-plugins = Cython.Coverage
+plugins = coverage_plugin
diff --git a/.github/workflows/buildwheel.yml b/.github/workflows/buildwheel.yml
index 90bf7810..a285cfed 100644
--- a/.github/workflows/buildwheel.yml
+++ b/.github/workflows/buildwheel.yml
@@ -149,11 +149,9 @@ jobs:
           python-version: '3.12'
       - run: sudo apt-get update
       - run: sudo apt-get install libflint-dev
-      - run: pip install cython setuptools coverage
+      - run: pip install git+https://github.com/oscarbenjamin/cython.git@pr_relative_paths
+      - run: pip install -r requirements-dev.txt
       - run: bin/coverage.sh
-        env:
-          PYTHONPATH: src
-      - run: coverage report --sort=cover
 
   # Run SymPy test suite against python-flint master
   test_sympy:
diff --git a/bin/coverage.sh b/bin/coverage.sh
index 65f189a8..1c729377 100755
--- a/bin/coverage.sh
+++ b/bin/coverage.sh
@@ -1,42 +1,21 @@
 #!/bin/bash
 #
-# Note: cython's Cython/Coverage.py fails for pyx files that are included in
-# other pyx files. This gives the following error:
+# This needs a patched Cython:
 #
-#   $ coverage report -m
-#   Plugin 'Cython.Coverage.Plugin' did not provide a file reporter for
-#   '.../python-flint/src/flint/fmpz.pyx'.
+#   pip install git+https://github.com/oscarbenjamin/cython.git@pr_relative_paths
 #
-# A patch to the file is needed:
+# That patch has been submitted as a pull request:
 #
-#  --- Coverage.py.backup   2022-12-09 17:36:35.387690467 +0000
-#  +++ Coverage.py 2022-12-09 17:08:06.282516837 +0000
-#  @@ -172,7 +172,9 @@ class Plugin(CoveragePlugin):
-#          else:
-#              c_file, _ = self._find_source_files(filename)
-#              if not c_file:
-# -                return None
-# +                c_file = os.path.join(os.path.dirname(filename), 'pyflint.c')
-# +                if not os.path.exists(c_file):
-# +                    return None
-#              rel_file_path, code = self._read_source_lines(c_file, filename)
-#              if code is None:
-#                  return None  # no source found
+#   https://github.com/cython/cython/pull/6341
 #
+# Arguments to this script are passed to python -m flint.test e.g. to skip
+# doctests and run in quiet mode:
+#
+#    bin/coverage.sh -qt
 #
-
 set -o errexit
 
-source bin/activate
-
-export PYTHON_FLINT_COVERAGE=true
-
-# Force a rebuild of everything with coverage tracing enabled:
-# touch src/flint/flintlib/*
-
-python setup.py build_ext --inplace
-
-coverage run -m flint.test $@
-
-#coverage report -m
+meson setup build -Dcoverage=true
+spin run -- coverage run -m flint.test $@
+coverage report -m --sort=cover
 coverage html
diff --git a/coverage_plugin.py b/coverage_plugin.py
new file mode 100644
index 00000000..8382dc26
--- /dev/null
+++ b/coverage_plugin.py
@@ -0,0 +1,184 @@
+"""
+A Cython plugin for coverage.py suitable for a spin/meson project.
+
+This follows the same general approach as Cython's coverage plugin and uses the
+Cython plugin for parsing the C files. The difference here is that files are
+laid out very differently in a meson project. Assuming meson makes it a lot
+easier to find all the C files because we can just parse the build.ninja file.
+
+https://coverage.readthedocs.io/en/latest/api_plugin.html
+https://github.com/cython/cython/blob/master/Cython/Coverage.py
+"""
+import re
+from collections import defaultdict
+
+from coverage.plugin import CoveragePlugin, FileTracer, FileReporter
+
+from functools import cache
+from pathlib import Path
+
+
+# Paths used by spin/meson in a src-layout:
+root_dir = Path(__file__).parent
+build_dir = root_dir / 'build'
+build_install_dir = root_dir / 'build-install'
+src_dir = root_dir / 'src'
+
+
+def get_ninja_build_rules():
+    """Read all build rules from build.ninja."""
+    rules = []
+    with open(build_dir / 'build.ninja') as build_ninja:
+        for line in build_ninja:
+            line = line.strip()
+            if line.startswith('build '):
+                line = line[len('build '):]
+                target, rule = line.split(': ')
+                if target == 'PHONY':
+                    continue
+                compiler, *srcfiles = rule.split(' ')
+                # target is a path relative to the build directory. We will
+                # turn that into an absolute path so that all paths in target
+                # and srcfiles are absolute.
+                target = str(build_dir / target)
+                rule = (target, compiler, srcfiles)
+                rules.append(rule)
+    return rules
+
+
+def get_cython_build_rules():
+    """Get all Cython build rules."""
+    cython_rules = []
+
+    for target, compiler, srcfiles in get_ninja_build_rules():
+        if compiler == 'cython_COMPILER':
+            assert target.endswith('.c')
+            assert len(srcfiles) == 1 and srcfiles[0].endswith('.pyx')
+            c_file = target
+            [cython_file] = srcfiles
+            cython_rules.append((c_file, cython_file))
+
+    return cython_rules
+
+
+@cache
+def parse_all_cfile_lines():
+    """Parse all generated C files from the build directory."""
+    #
+    # Each .c file can include code generated from multiple Cython files (e.g.
+    # because of .pxd files) being cimported. Each Cython file can contribute
+    # to more than one .c file. Here we parse all .c files and then collect
+    # together all the executable lines from all of the Cython files into a
+    # dict like this:
+    #
+    #   {filename: {lineno: linestr, ...}, ...}
+    #
+    # This function is cached because it only needs calling once and is
+    # expensive.
+    #
+    all_code_lines = {}
+
+    for c_file, _ in get_cython_build_rules():
+
+        cfile_lines = parse_cfile_lines(c_file)
+
+        for cython_file, line_map in cfile_lines.items():
+            if cython_file == '(tree fragment)':
+                continue
+            elif cython_file in all_code_lines:
+                # Possibly need to merge the lines?
+                assert all_code_lines[cython_file] == line_map
+            else:
+                all_code_lines[cython_file] = line_map
+
+    return all_code_lines
+
+
+def parse_cfile_lines(c_file):
+    """Use Cython's coverage plugin to parse the C code."""
+    from Cython.Coverage import Plugin
+    return Plugin()._parse_cfile_lines(c_file)
+
+
+class Plugin(CoveragePlugin):
+    """A coverage plugin for a spin/meson project with Cython code."""
+
+    def file_tracer(self, filename):
+        """Find a tracer for filename to handle trace events."""
+        path = Path(filename)
+
+        if path.suffix in ('.pyx', '.pxd') and root_dir in path.parents:
+            # A .pyx file from the src directory. The path has src
+            # stripped out and is not a real absolute path but it looks
+            # like one. Remove the root prefix and then we have a path
+            # relative to src_dir.
+            srcpath = path.relative_to(root_dir)
+            return CyFileTracer(srcpath)
+        else:
+            # All sorts of paths come here and we reject them
+            return None
+
+    def file_reporter(self, filename):
+        """Return a file reporter for filename."""
+        srcfile = Path(filename).relative_to(src_dir)
+        return CyFileReporter(srcfile)
+
+
+class CyFileTracer(FileTracer):
+    """File tracer for Cython files (.pyx,.pxd)."""
+
+    def __init__(self, srcpath):
+        assert (src_dir / srcpath).exists()
+        self.srcpath = srcpath
+
+    def source_filename(self):
+        return self.srcpath
+
+    def has_dynamic_source_filename(self):
+        return True
+
+    def dynamic_source_filename(self, filename, frame):
+        """Get filename from frame and return abspath to file."""
+        # What is returned here needs to match CyFileReporter.filename
+        path = frame.f_code.co_filename
+        return self.get_source_filename(path)
+
+    # This is called for every traced line. Cache it:
+    @staticmethod
+    @cache
+    def get_source_filename(filename):
+        """Get src-relative path for filename from trace event."""
+        path = src_dir / filename
+        assert src_dir in path.parents
+        assert path.exists()
+        return str(path)
+
+
+class CyFileReporter(FileReporter):
+    """File reporter for Cython or Python files (.pyx,.pxd,.py)."""
+
+    def __init__(self, srcpath):
+        abspath = (src_dir / srcpath)
+        assert abspath.exists()
+
+        # filepath here needs to match dynamic_source_filename
+        super().__init__(str(abspath))
+
+        self.srcpath = srcpath
+
+    def relative_filename(self):
+        """Path displayed in the coverage reports."""
+        return str(self.srcpath)
+
+    def lines(self):
+        """Set of line numbers for possibly traceable lines."""
+        srcpath = str(self.srcpath)
+        all_line_maps = parse_all_cfile_lines()
+        line_map = all_line_maps[srcpath]
+        return set(line_map)
+
+
+def coverage_init(reg, options):
+    plugin = Plugin()
+    reg.add_configurer(plugin)
+    reg.add_file_tracer(plugin)
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 536a010f..1429700e 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -1,4 +1,5 @@
 cython
+ninja
 spin
 meson
 meson-python