diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index fd9d618d1f..ff85414834 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -1163,11 +1163,25 @@ def _add_dependency_cpp_headers(self, dep_root, extra_dirs=None):
         if extra_dirs is None:
             extra_dirs = ()
 
-        header_dirs = ["include"]
-        header_dirs = unique_ordered_extend(header_dirs, extra_dirs)
+        for env_var in SEARCH_PATH['cpp_headers'][self.search_path['cpp_headers']]:
+            header_dirs = []
+            # take into account all $*PATH environment variables for dependencies
+            for key in [y for x in SEARCH_PATH['cpp_headers'].values() for y in x if y.endswith('PATH')]:
+                val = os.getenv(key)
+                if val:
+                    self.log.debug(f"${key} when determining subdirs of {dep_root} to retain for ${env_var}: {val}")
+                    paths = val.split(':')
+                    matching_paths = [p for p in paths if p.startswith(dep_root)]
+                    subdirs = [os.path.relpath(p, dep_root) for p in matching_paths]
+                    self.log.debug(f"Subdirectories of {dep_root} to add to ${env_var}: {subdirs}")
+                    header_dirs.extend(os.path.relpath(p, dep_root) for p in matching_paths)
+                else:
+                    self.log.debug(f"${key} not defined, not used to find subdirs of {dep_root} to use for ${env_var}")
+
+            # take into account extra_dirs + only retain unique entries
+            header_dirs = unique_ordered_extend(header_dirs, extra_dirs)
 
-        for env_var in SEARCH_PATH["cpp_headers"][self.search_path["cpp_headers"]]:
-            self.log.debug("Adding header paths to toolchain variable '%s': %s", env_var, dep_root)
+            self.log.info(f"Adding header paths to toolchain variable '{env_var}': {dep_root} (subdirs: {header_dirs})")
             self.variables.append_subdirs(env_var, dep_root, subdirs=header_dirs)
 
     def _add_dependency_linker_paths(self, dep_root, extra_dirs=None):
diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 085a6c947f..97f769126c 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -3745,9 +3745,13 @@ def test_exts_deps_build_env(self):
 
         zlib_root = os.path.join(self.test_prefix, 'software', 'zlib', zlib_fn)
         write_file(os.path.join(zlib_root, 'include', 'zlib.h'), '')
+        write_file(os.path.join(zlib_root, 'include', 'zlib', 'common.h'), '')
 
         zlib_mod_txt = read_file(zlib_mod_file)
         zlib_mod_txt = re.sub("set root.*", f"set root {zlib_root}", zlib_mod_txt)
+        # add statement to inject extra subdirectory to $CPATH,
+        # which is supposed to be retained in build environment
+        zlib_mod_txt += '\nprepend-path\tCPATH\t$root/include/zlib'
 
         test_mods = os.path.join(self.test_prefix, 'modules')
         test_zlib_mod_file = os.path.join(test_mods, 'zlib', zlib_fn)
@@ -3765,7 +3769,9 @@ def test_exts_deps_build_env(self):
                 test_ec,
                 '--rebuild',
                 f'--search-path-cpp-headers={search_path_cpp_headers}',
+                '--debug',
             ]
+            os.environ['C_INCLUDE_PATH'] = '/usr/local/include'
             with self.mocked_stdout_stderr():
                 with self.log_to_testlogfile():
                     self.eb_main(args, raise_error=True, do_build=True, verbose=True)
@@ -3778,7 +3784,14 @@ def test_exts_deps_build_env(self):
 
             # check whether $C_INCLUDE_PATH is correctly set in build environment of 'bar' extension
             for env_var in env_vars[search_path_cpp_headers]:
-                regex = re.compile(f"^{env_var}=.*/software/zlib/{zlib_fn}/include$", re.M)
+                # both 'include' and 'include/zlib' subdirectories should be retained
+                paths = [f'software/zlib/{zlib_fn}/include/zlib', f'software/zlib/{zlib_fn}/include']
+                if env_var.endswith('PATH'):
+                    regex = re.compile(f'^{env_var}=' + ':'.join('[^ ]+/' + p for p in paths) + '$', re.M)
+                elif env_var == 'CPPFLAGS':
+                    regex = re.compile(f'^{env_var}=' + ' '.join('-I/[^ ]+/' + p for p in paths) + '$', re.M)
+                else:
+                    self.fail(f"Unknown type of environment variable: ${env_var}")
                 self.assertTrue(regex.search(log_txt), f"Pattern '{regex.pattern}' not found in log output")