diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 40e4c2762b..6bc7018a05 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9499,10 +9499,10 @@ (define-public sailfish
 
              ;; Ensure that Eigen headers can be found
              (setenv "CPLUS_INCLUDE_PATH"
-                     (string-append (assoc-ref inputs "eigen")
-                                    "/include/eigen3:"
-                                    (or (getenv "CPLUS_INCLUDE_PATH") "")))
-             #t)))))
+                     (string-append (search-input-directory
+                                     inputs "/include/eigen3")
+                                    ":"
+                                    (or (getenv "CPLUS_INCLUDE_PATH") ""))))))))
     (inputs
      `(("boost" ,boost)
        ("eigen" ,eigen)
@@ -12456,10 +12456,9 @@ (define-public nanopolish
            (add-after 'unpack 'find-eigen
              (lambda* (#:key inputs #:allow-other-keys)
                (setenv "CPATH"
-                       (string-append (assoc-ref inputs "eigen")
-                                      "/include/eigen3:"
-                                      (or (getenv "CPATH") "")))
-               #t))
+                       (string-append
+                        (search-input-directory inputs "/include/eigen3")
+                        ":" (or (getenv "CPATH") "")))))
            (delete 'configure)
            (replace 'install
              (lambda* (#:key outputs #:allow-other-keys)
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 367d7495ce..74742df442 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1732,7 +1732,7 @@ (define-public tensorflow
                 (string-append (getcwd) "/eigen-src/"))
                ;; Take Eigen headers from our own package.
                (("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/external/eigen_archive")
-                (string-append (assoc-ref inputs "eigen") "/include/eigen3")))
+                (search-input-directory inputs "/include/eigen3")))
 
              ;; Correct the RUNPATH of ops libraries generated for Python.
              ;; TODO: this doesn't work :(