diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 46968784d08..52c5a8d118f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -22463,11 +22463,7 @@ sequences to accelerate the alignment process.")
       #~(list "-DZIG=OFF"
               "-DTABIXPP_LOCAL=OFF"
               "-DTABIX_FOUND=ON"
-              "-DWFA_GITMODULE=OFF"
-              (string-append "-DPKG_CONFIG_EXECUTABLE="
-                             (search-input-file
-                              %build-inputs (string-append
-                                             "/bin/" #$(pkg-config-for-target)))))
+              "-DWFA_GITMODULE=OFF")
       #:tests? #f                       ; no tests
       #:phases
       #~(modify-phases %standard-phases
diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm
index ecd19ace02e..4edae46bfe5 100644
--- a/gnu/packages/cpp.scm
+++ b/gnu/packages/cpp.scm
@@ -1021,17 +1021,6 @@ utilities used across the hypr* ecosystem.")
                (base32
                 "0n64jq9jdabyx76sax0fb45jg92708488733c2m6zsf84r6nv2g7"))))
     (build-system cmake-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'fix-cross-compilation
-            (lambda _
-              (substitute* "CMakeLists.txt"
-                (("find_package.PkgConfig" all)
-                 (string-append
-                  "set(PKG_CONFIG_EXECUTABLE " #$(pkg-config-for-target) ")\n"
-                  all))))))))
     (native-inputs (list gcc-15 pkg-config))
     (inputs (list hyprutils))
     (home-page "https://wiki.hypr.land/Hypr-Ecosystem/hyprlang/")
@@ -1055,18 +1044,6 @@ language used in Hyprland.")
                (base32
                 "1ymiqzncppdik8lw3ad7xaqig6c7bjcy7crcwbq3rjfk2hrc8rmc"))))
     (build-system cmake-build-system)
-    (arguments
-     (list
-      #:tests? #f ; No tests in Release build type
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'fix-cross-compilation
-            (lambda _
-              (substitute* "CMakeLists.txt"
-                (("find_package.PkgConfig" all)
-                 (string-append
-                  "set(PKG_CONFIG_EXECUTABLE " #$(pkg-config-for-target) ")\n"
-                  all))))))))
     (native-inputs (list gcc-15 pkg-config))
     (inputs (list pixman))
     (home-page "https://github.com/hyprwm/hyprutils")
diff --git a/gnu/packages/debian.scm b/gnu/packages/debian.scm
index 1a58474fa6a..c65c6d90cb7 100644
--- a/gnu/packages/debian.scm
+++ b/gnu/packages/debian.scm
@@ -646,12 +646,6 @@ debian/copyright for more information.")))))
     (native-inputs (list pkg-config))
     (arguments
      (list
-      #:configure-flags
-      #~(list
-         (string-append "-DPKG_CONFIG_EXECUTABLE="
-                        (search-input-file
-                         %build-inputs (string-append
-                                        "/bin/" #$(pkg-config-for-target)))))
       #:tests? #f ;Tests are "for development only".
       #:phases #~(modify-phases %standard-phases
                    ;; We want to provide good defaults. Here apt-cacher-ng is built
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index b84ceceb6a0..81190ab0c44 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -8083,17 +8083,10 @@ from the ntfs-3g package.  It is meant to be used in initrds.")
        ;; Upstream uses the "ninja" build system and encourage distros
        ;; to do the same for consistency.
        #:generator "Ninja"
-       #:configure-flags (list ,@(if (%current-target-system)
-                                     `((string-append
-                                        "-DPKG_CONFIG_EXECUTABLE="
-                                        (search-input-file
-                                         %build-inputs
-                                         (string-append "/bin/"
-                                                        ,(pkg-config-for-target)))))
-                                     '())
-                               (string-append "-DRST2MAN_EXECUTABLE="
-                                              (search-input-file
-                                               %build-inputs "/bin/rst2man.py")))))
+       #:configure-flags
+       (list (string-append "-DRST2MAN_EXECUTABLE="
+                            (search-input-file
+                             %build-inputs "/bin/rst2man.py")))))
     (native-inputs
      (list pkg-config python-wrapper python-docutils-0.19)) ;for 'rst2man'
     (inputs
diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index c08f77f75bb..8b307fe9956 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -224,10 +224,6 @@ used as a drop-in substitute for @code{libfec}.")
       #:tests? #f
       #:configure-flags
       #~(list
-         (string-append "-DPKG_CONFIG_EXECUTABLE="
-                        (search-input-file
-                         %build-inputs
-                         (string-append "/bin/" #$(pkg-config-for-target))))
          (string-append "-DUDEV_RULES_INSTALL_DIR="
                         #$output "/lib/udev/rules.d")
          "-DOSX_PACKAGE=off"
diff --git a/gnu/packages/security-token.scm b/gnu/packages/security-token.scm
index b68e1068b05..e56c3405865 100644
--- a/gnu/packages/security-token.scm
+++ b/gnu/packages/security-token.scm
@@ -1123,12 +1123,7 @@ phone and a running pcscd service are required.")
     (arguments
      (list
       #:configure-flags
-      #~(list (string-append
-               "-DPKG_CONFIG_EXECUTABLE="
-               (search-input-file %build-inputs
-                                  (string-append
-                                   "/bin/" #$(pkg-config-for-target))))
-              (string-append "-DUDEV_RULES_DIR=" #$output "/lib/udev/rules.d"))
+      #~(list (string-append "-DUDEV_RULES_DIR=" #$output "/lib/udev/rules.d"))
       ;; regress tests enabled only for debug builds
       #:tests? #f))
     (synopsis "Library functionality and command-line tools for FIDO devices")
diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 9ff85282677..47861508336 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -1266,15 +1266,7 @@ other git-like projects such as @code{libgit2}.")
             (list "-DUSE_NTLMCLIENT=OFF" ;TODO: package this
                   "-DREGEX_BACKEND=pcre2"
                   "-DUSE_HTTP_PARSER=system"
-                  "-DUSE_SSH=ON" ; cmake fails to find libssh if this is missing
-                  ,@(if (%current-target-system)
-                        `((string-append
-                           "-DPKG_CONFIG_EXECUTABLE="
-                           (search-input-file
-                            %build-inputs
-                            (string-append "/bin/" ,(%current-target-system)
-                                           "-pkg-config"))))
-                        '())))
+                  "-DUSE_SSH=ON")) ; cmake fails to find libssh if this is missing
        #:phases
        (modify-phases %standard-phases
          ,@(if (or (target-arm32?) (target-hurd?))
@@ -1365,15 +1357,7 @@ write native speed custom Git applications in any language with bindings.")
         `(list "-DUSE_NTLMCLIENT=OFF" ;TODO: package this
                "-DREGEX_BACKEND=pcre2"
                "-DUSE_HTTP_PARSER=system"
-               "-DUSE_SSH=ON" ; cmake fails to find libssh if this is missing
-               ,@(if (%current-target-system)
-                     `((string-append
-                        "-DPKG_CONFIG_EXECUTABLE="
-                        (search-input-file
-                         %build-inputs
-                         (string-append "/bin/" ,(%current-target-system)
-                                        "-pkg-config"))))
-                     '())))))))
+               "-DUSE_SSH=ON")))))) ; cmake fails to find libssh if this is missing
 
 (define-public libgit2-1.6
   (package
diff --git a/gnu/packages/vulkan.scm b/gnu/packages/vulkan.scm
index ea7cdc3ef59..b38d472b56d 100644
--- a/gnu/packages/vulkan.scm
+++ b/gnu/packages/vulkan.scm
@@ -402,12 +402,7 @@ Enhanced Subpixel Morphological Anti-Aliasing
                                        (search-input-directory
                                         %build-inputs "include/vulkan"))))
               #$@(if (%current-target-system)
-                     #~("-DBUILD_TESTS=OFF" "-DUSE_GAS=OFF"
-                        (string-append
-                         "-DPKG_CONFIG_EXECUTABLE="
-                         (search-input-file
-                          %build-inputs
-                          (string-append "bin/" #$(pkg-config-for-target)))))
+                     #~("-DBUILD_TESTS=OFF" "-DUSE_GAS=OFF")
                      #~("-DBUILD_TESTS=ON")))
       #:phases
       #~(modify-phases %standard-phases