diff --git a/Misc/NEWS.d/next/Build/2022-07-26-18-13-34.gh-issue-94801.9fREfy.rst b/Misc/NEWS.d/next/Build/2022-07-26-18-13-34.gh-issue-94801.9fREfy.rst
new file mode 100644
index 000000000000..a58be30e81b0
--- /dev/null
+++ b/Misc/NEWS.d/next/Build/2022-07-26-18-13-34.gh-issue-94801.9fREfy.rst
@@ -0,0 +1,2 @@
+Fix a regression in ``configure`` script that caused some header checks to
+ignore custom ``CPPFLAGS``. The regression was introduced in :gh:`94802`.
diff --git a/configure b/configure
index 378103a641a8..19316baa6ee1 100755
--- a/configure
+++ b/configure
@@ -11180,7 +11180,7 @@ save_LDFLAGS=$LDFLAGS
 save_LIBS=$LIBS
 
 
-        CPPFLAGS="$CFLAGS $LIBUUID_CFLAGS"
+        CPPFLAGS="$CPPFLAGS $LIBUUID_CFLAGS"
         LDFLAGS="$LDFLAGS $LIBUUID_LIBS"
         for ac_header in uuid/uuid.h
 do :
@@ -11309,7 +11309,7 @@ save_LDFLAGS=$LDFLAGS
 save_LIBS=$LIBS
 
 
-        CPPFLAGS="$CFLAGS $LIBUUID_CFLAGS"
+        CPPFLAGS="$CPPFLAGS $LIBUUID_CFLAGS"
         LDFLAGS="$LDFLAGS $LIBUUID_LIBS"
         for ac_header in uuid/uuid.h
 do :
@@ -12352,7 +12352,7 @@ save_LDFLAGS=$LDFLAGS
 save_LIBS=$LIBS
 
 
-    CPPFLAGS="$LIBNSL_CFLAGS $CFLAGS"
+    CPPFLAGS="$CPPFLAGS $LIBNSL_CFLAGS"
     for ac_header in rpc/rpc.h
 do :
   ac_fn_c_check_header_mongrel "$LINENO" "rpc/rpc.h" "ac_cv_header_rpc_rpc_h" "$ac_includes_default"
@@ -12485,7 +12485,7 @@ save_LDFLAGS=$LDFLAGS
 save_LIBS=$LIBS
 
 
-  CPPFLAGS="$LIBSQLITE3_CFLAGS $CFLAGS"
+  CPPFLAGS="$CPPFLAGS $LIBSQLITE3_CFLAGS"
   LDFLAGS="$LIBSQLITE3_LIBS $LDFLAGS"
 
   ac_fn_c_check_header_mongrel "$LINENO" "sqlite3.h" "ac_cv_header_sqlite3_h" "$ac_includes_default"
@@ -13431,7 +13431,7 @@ save_LDFLAGS=$LDFLAGS
 save_LIBS=$LIBS
 
 
-  CPPFLAGS="$TCLTK_CFLAGS $CFLAGS"
+  CPPFLAGS="$CPPFLAGS $TCLTK_CFLAGS"
   LIBS="$TCLTK_LIBS $LDFLAGS"
 
   cat confdefs.h - <<_ACEOF >conftest.$ac_ext
@@ -13496,7 +13496,7 @@ save_LDFLAGS=$LDFLAGS
 save_LIBS=$LIBS
 
 
-  CPPFLAGS="$GDBM_CFLAGS $CFLAGS"
+  CPPFLAGS="$CPPFLAGS $GDBM_CFLAGS"
   LDFLAGS="$GDBM_LIBS $LDFLAGS"
   for ac_header in gdbm.h
 do :
@@ -16020,7 +16020,7 @@ save_LDFLAGS=$LDFLAGS
 save_LIBS=$LIBS
 
 
-    CPPFLAGS="$CFLAGS $ZLIB_CFLAGS"
+    CPPFLAGS="$CPPFLAGS $ZLIB_CFLAGS"
     LDFLAGS="$LDFLAGS $ZLIB_LIBS"
     for ac_header in zlib.h
 do :
@@ -16150,7 +16150,7 @@ save_LDFLAGS=$LDFLAGS
 save_LIBS=$LIBS
 
 
-    CPPFLAGS="$CFLAGS $ZLIB_CFLAGS"
+    CPPFLAGS="$CPPFLAGS $ZLIB_CFLAGS"
     LDFLAGS="$LDFLAGS $ZLIB_LIBS"
     for ac_header in zlib.h
 do :
@@ -16368,7 +16368,7 @@ save_LDFLAGS=$LDFLAGS
 save_LIBS=$LIBS
 
 
-    CPPFLAGS="$CFLAGS $BZIP2_CFLAGS"
+    CPPFLAGS="$CPPFLAGS $BZIP2_CFLAGS"
     LDFLAGS="$LDFLAGS $BZIP2_LIBS"
     for ac_header in bzlib.h
 do :
@@ -16451,7 +16451,7 @@ save_LDFLAGS=$LDFLAGS
 save_LIBS=$LIBS
 
 
-    CPPFLAGS="$CFLAGS $BZIP2_CFLAGS"
+    CPPFLAGS="$CPPFLAGS $BZIP2_CFLAGS"
     LDFLAGS="$LDFLAGS $BZIP2_LIBS"
     for ac_header in bzlib.h
 do :
@@ -16598,7 +16598,7 @@ save_LDFLAGS=$LDFLAGS
 save_LIBS=$LIBS
 
 
-    CPPFLAGS="$CFLAGS $LIBLZMA_CFLAGS"
+    CPPFLAGS="$CPPFLAGS $LIBLZMA_CFLAGS"
     LDFLAGS="$LDFLAGS $LIBLZMA_LIBS"
     for ac_header in lzma.h
 do :
@@ -16681,7 +16681,7 @@ save_LDFLAGS=$LDFLAGS
 save_LIBS=$LIBS
 
 
-    CPPFLAGS="$CFLAGS $LIBLZMA_CFLAGS"
+    CPPFLAGS="$CPPFLAGS $LIBLZMA_CFLAGS"
     LDFLAGS="$LDFLAGS $LIBLZMA_LIBS"
     for ac_header in lzma.h
 do :
@@ -17508,7 +17508,7 @@ save_LDFLAGS=$LDFLAGS
 save_LIBS=$LIBS
 
 
-  CPPFLAGS="$LIBCRYPT_CFLAGS $CFLAGS"
+  CPPFLAGS="$CPPFLAGS $LIBCRYPT_CFLAGS"
   LIBS="$LIBCRYPT_LIBS $LIBS"
   { $as_echo "$as_me:${as_lineno-$LINENO}: checking for crypt or crypt_r" >&5
 $as_echo_n "checking for crypt or crypt_r... " >&6; }
diff --git a/configure.ac b/configure.ac
index 7d8c670da947..f1fa57055623 100644
--- a/configure.ac
+++ b/configure.ac
@@ -3378,7 +3378,7 @@ AS_VAR_IF([have_uuid], [missing], [
       AC_DEFINE([HAVE_UUID_GENERATE_TIME_SAFE], [1])
     ], [
       WITH_SAVE_ENV([
-        CPPFLAGS="$CFLAGS $LIBUUID_CFLAGS"
+        CPPFLAGS="$CPPFLAGS $LIBUUID_CFLAGS"
         LDFLAGS="$LDFLAGS $LIBUUID_LIBS"
         AC_CHECK_HEADERS([uuid/uuid.h], [
           PY_CHECK_LIB([uuid], [uuid_generate_time], [have_uuid=yes])
@@ -3730,7 +3730,7 @@ PKG_CHECK_MODULES([LIBNSL], [libnsl], [have_nis=yes], [
 
 AS_VAR_IF([have_nis], [yes], [
   WITH_SAVE_ENV([
-    CPPFLAGS="$LIBNSL_CFLAGS $CFLAGS"
+    CPPFLAGS="$CPPFLAGS $LIBNSL_CFLAGS"
     AC_CHECK_HEADERS([rpc/rpc.h])
   ])
 ])
@@ -3763,7 +3763,7 @@ AC_DEFUN([PY_CHECK_SQLITE_FUNC], [
 WITH_SAVE_ENV([
 dnl bpo-45774/GH-29507: The CPP check in AC_CHECK_HEADER can fail on FreeBSD,
 dnl hence CPPFLAGS instead of CFLAGS.
-  CPPFLAGS="$LIBSQLITE3_CFLAGS $CFLAGS"
+  CPPFLAGS="$CPPFLAGS $LIBSQLITE3_CFLAGS"
   LDFLAGS="$LIBSQLITE3_LIBS $LDFLAGS"
 
   AC_CHECK_HEADER([sqlite3.h], [
@@ -3867,7 +3867,7 @@ AS_CASE([$ac_sys_system],
 )
 
 WITH_SAVE_ENV([
-  CPPFLAGS="$TCLTK_CFLAGS $CFLAGS"
+  CPPFLAGS="$CPPFLAGS $TCLTK_CFLAGS"
   LIBS="$TCLTK_LIBS $LDFLAGS"
 
   AC_LINK_IFELSE([
@@ -3909,7 +3909,7 @@ dnl NOTE: gdbm does not provide a pkgconf file.
 AC_ARG_VAR([GDBM_CFLAGS], [C compiler flags for gdbm])
 AC_ARG_VAR([GDBM_LIBS], [additional linker flags for gdbm])
 WITH_SAVE_ENV([
-  CPPFLAGS="$GDBM_CFLAGS $CFLAGS"
+  CPPFLAGS="$CPPFLAGS $GDBM_CFLAGS"
   LDFLAGS="$GDBM_LIBS $LDFLAGS"
   AC_CHECK_HEADERS([gdbm.h], [
     AC_CHECK_LIB([gdbm], [gdbm_open], [
@@ -4734,7 +4734,7 @@ PKG_CHECK_MODULES([ZLIB], [zlib >= 1.2.0], [
   AC_DEFINE([HAVE_ZLIB_COPY], [1])
 ], [
   WITH_SAVE_ENV([
-    CPPFLAGS="$CFLAGS $ZLIB_CFLAGS"
+    CPPFLAGS="$CPPFLAGS $ZLIB_CFLAGS"
     LDFLAGS="$LDFLAGS $ZLIB_LIBS"
     AC_CHECK_HEADERS([zlib.h], [
       PY_CHECK_LIB([z], [gzread], [have_zlib=yes], [have_zlib=no])
@@ -4758,7 +4758,7 @@ PY_CHECK_EMSCRIPTEN_PORT([BZIP2], [-sUSE_BZIP2])
 
 PKG_CHECK_MODULES([BZIP2], [bzip2], [have_bzip2=yes], [
   WITH_SAVE_ENV([
-    CPPFLAGS="$CFLAGS $BZIP2_CFLAGS"
+    CPPFLAGS="$CPPFLAGS $BZIP2_CFLAGS"
     LDFLAGS="$LDFLAGS $BZIP2_LIBS"
     AC_CHECK_HEADERS([bzlib.h], [
       AC_CHECK_LIB([bz2], [BZ2_bzCompress], [have_bzip2=yes], [have_bzip2=no])
@@ -4772,7 +4772,7 @@ PKG_CHECK_MODULES([BZIP2], [bzip2], [have_bzip2=yes], [
 
 PKG_CHECK_MODULES([LIBLZMA], [liblzma], [have_liblzma=yes], [
   WITH_SAVE_ENV([
-    CPPFLAGS="$CFLAGS $LIBLZMA_CFLAGS"
+    CPPFLAGS="$CPPFLAGS $LIBLZMA_CFLAGS"
     LDFLAGS="$LDFLAGS $LIBLZMA_LIBS"
     AC_CHECK_HEADERS([lzma.h], [
       AC_CHECK_LIB([lzma], [lzma_easy_encoder], [have_liblzma=yes], [have_liblzma=no])
@@ -4864,7 +4864,7 @@ PKG_CHECK_MODULES([LIBCRYPT], [libxcrypt >= 3.1.1], [
 ])
 
 WITH_SAVE_ENV([
-  CPPFLAGS="$LIBCRYPT_CFLAGS $CFLAGS"
+  CPPFLAGS="$CPPFLAGS $LIBCRYPT_CFLAGS"
   LIBS="$LIBCRYPT_LIBS $LIBS"
   AC_CACHE_CHECK([for crypt or crypt_r], [ac_cv_crypt_crypt], [
     AC_LINK_IFELSE([AC_LANG_PROGRAM([