diff --git a/setuptools/_distutils/command/build_ext.py b/setuptools/_distutils/command/build_ext.py
index 06d949a..0dee0fe 100644
--- a/setuptools/_distutils/command/build_ext.py
+++ b/setuptools/_distutils/command/build_ext.py
@@ -209,6 +209,14 @@ class build_ext(Command):
         elif isinstance(self.rpath, str):
             self.rpath = self.rpath.split(os.pathsep)
 
+        prefix = os.path.normpath(sys.prefix)
+        vcpkg_prefix = os.path.dirname(os.path.dirname(prefix)) # Add debug compile?
+
+        if self.debug:
+            self.library_dirs.append(os.path.join(vcpkg_prefix, 'debug', 'lib'))
+        else:
+            self.library_dirs.append(os.path.join(vcpkg_prefix, 'lib'))
+
         # for extensions under windows use different directories
         # for Release and Debug builds.
         # also Python's library directory must be appended to library_dirs
@@ -216,9 +224,9 @@ class build_ext(Command):
             # the 'libs' directory is for binary installs - we assume that
             # must be the *native* platform.  But we don't really support
             # cross-compiling via a binary install anyway, so we let it go.
-            self.library_dirs.append(os.path.join(sys.exec_prefix, 'libs'))
-            if sys.base_exec_prefix != sys.prefix:  # Issue 16116
-                self.library_dirs.append(os.path.join(sys.base_exec_prefix, 'libs'))
+            # self.library_dirs.append(os.path.join(sys.exec_prefix, 'libs'))
+            # if sys.base_exec_prefix != sys.prefix:  # Issue 16116
+            #    self.library_dirs.append(os.path.join(sys.base_exec_prefix, 'libs'))
             if self.debug:
                 self.build_temp = os.path.join(self.build_temp, "Debug")
             else:
diff --git a/setuptools/_distutils/sysconfig.py b/setuptools/_distutils/sysconfig.py
index 1a38e9f..2c8174d 100644
--- a/setuptools/_distutils/sysconfig.py
+++ b/setuptools/_distutils/sysconfig.py
@@ -191,18 +191,21 @@ def _get_python_inc_from_config(plat_specific, spec_prefix):
 def _get_python_inc_posix_prefix(prefix):
     implementation = 'pypy' if IS_PYPY else 'python'
     python_dir = implementation + get_python_version() + build_flags
-    return os.path.join(prefix, "include", python_dir)
+    vcpkg_prefix = os.path.dirname(os.path.dirname(prefix))
+    return os.path.join(vcpkg_prefix, "include", python_dir)
 
 
 def _get_python_inc_nt(prefix, spec_prefix, plat_specific):
+    vcpkg_prefix = os.path.dirname(os.path.dirname(prefix))
+    python_dir = 'python' + get_python_version()
     if python_build:
         # Include both include dirs to ensure we can find pyconfig.h
         return (
-            os.path.join(prefix, "include")
+            os.path.join(vcpkg_prefix, "include", python_dir)
             + os.path.pathsep
             + os.path.dirname(sysconfig.get_config_h_filename())
         )
-    return os.path.join(prefix, "include")
+    return os.path.join(vcpkg_prefix, "include", python_dir)
 
 
 # allow this behavior to be monkey-patched. Ref pypa/distutils#2.