diff --git a/gnu/local.mk b/gnu/local.mk
index 6a1e459e4e..0016ac12af 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1375,6 +1375,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/lierolibre-newer-libconfig.patch		\
   %D%/packages/patches/lierolibre-remove-arch-warning.patch	\
   %D%/packages/patches/lierolibre-try-building-other-arch.patch	\
+  %D%/packages/patches/lightgbm-python-use-system-lib-lightgbm.patch \
+  %D%/packages/patches/lightgbm-use-system-libraries.patch	\
   %D%/packages/patches/linbox-fix-pkgconfig.patch		\
   %D%/packages/patches/linkchecker-tests-require-network.patch	\
   %D%/packages/patches/linphone-desktop-without-sdk.patch           \
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index ead47a534a..1a3f647dde 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -56,6 +56,7 @@
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cmake)
+  #:use-module (gnu packages cpp)
   #:use-module (gnu packages cran)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages dejagnu)
@@ -70,8 +71,10 @@
   #:use-module (gnu packages mpi)
   #:use-module (gnu packages ocaml)
   #:use-module (gnu packages onc-rpc)
+  #:use-module (gnu packages opencl)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages pretty-print)
   #:use-module (gnu packages protobuf)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-build)
@@ -1058,33 +1061,39 @@ main intended application of Autograd is gradient-based optimization.")
 (define-public lightgbm
   (package
     (name "lightgbm")
-    (version "2.0.12")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                     (url "https://github.com/Microsoft/LightGBM")
-                     (commit (string-append "v" version))))
-              (sha256
-               (base32
-                "0jlvyn7k81dzrh9ij3zw576wbgiwmmr26rzpdxjn1dbpc3njpvzi"))
-              (file-name (git-file-name name version))))
+    (version "3.2.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Microsoft/LightGBM")
+             (commit (string-append "v" version))))
+       (patches
+        (search-patches "lightgbm-use-system-libraries.patch"
+                        "lightgbm-python-use-system-lib-lightgbm.patch"))
+       (sha256
+        (base32 "1fchiiwl3pz1kpi0kbfanif6c6b688wmmjjbqz4ff4djc6g2sg7z"))
+       (file-name (git-file-name name version))))
     (native-inputs
-     `(("python-pytest" ,python-pytest)
-       ("python-nose" ,python-nose)))
+     `(("googletest" ,googletest)
+       ("opencl-headers" ,opencl-headers)))
     (inputs
-     `(("openmpi" ,openmpi)))
-    (propagated-inputs
-     `(("python-numpy" ,python-numpy)
-       ("python-scipy" ,python-scipy)))
+     `(("boost" ,boost)
+       ("eigen" ,eigen)
+       ("fast-double-parser" ,fast-double-parser)
+       ("fmt" ,fmt)
+       ("ocl-icd" ,ocl-icd)
+       ("openmpi" ,openmpi)))
     (arguments
-     `(#:configure-flags
-       '("-DUSE_MPI=ON")
-       #:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda _
-             (with-directory-excursion "../source"
-               (invoke "pytest" "tests/c_api_test/test_.py")))))))
+     `(;; FIXME: With 'find_package(GTest CONFIG)' (default), googletest
+       ;; is not found by CMake.  If we replace CONFIG with REQUIRED, the
+       ;; test files fail to link with googletest in the build phase.
+       #:tests? #f
+       #:test-target "testlightgbm"
+       #:configure-flags
+       (list "-DBUILD_CPP_TEST=OFF"
+             "-DUSE_GPU=ON" ;using OpenCL
+             "-DUSE_MPI=ON")))
     (build-system cmake-build-system)
     (home-page "https://github.com/Microsoft/LightGBM")
     (synopsis "Gradient boosting framework based on decision tree algorithms")
diff --git a/gnu/packages/patches/lightgbm-python-use-system-lib-lightgbm.patch b/gnu/packages/patches/lightgbm-python-use-system-lib-lightgbm.patch
new file mode 100644
index 0000000000..69cb721daa
--- /dev/null
+++ b/gnu/packages/patches/lightgbm-python-use-system-lib-lightgbm.patch
@@ -0,0 +1,74 @@
+From c73be84d8ec6ac71dfdaa71b7943ae344f5d7cde Mon Sep 17 00:00:00 2001
+From: Vinicius Monego <monego@posteo.net>
+Date: Tue, 1 Jun 2021 00:24:38 -0300
+Subject: [PATCH] Use system lib_lightgbm.
+
+---
+ python-package/lightgbm/libpath.py |  4 ++++
+ python-package/setup.py            | 12 ++++++++----
+ 2 files changed, 12 insertions(+), 4 deletions(-)
+
+diff --git a/python-package/lightgbm/libpath.py b/python-package/lightgbm/libpath.py
+index 6533792..27af2b9 100644
+--- a/python-package/lightgbm/libpath.py
++++ b/python-package/lightgbm/libpath.py
+@@ -17,8 +17,12 @@ def find_lib_path() -> List[str]:
+         # we don't need lib_lightgbm while building docs
+         return []
+ 
++    # This variable will be set during substitution.
++    lib_lightgbm_path = ''
++
+     curr_path = os.path.dirname(os.path.abspath(os.path.expanduser(__file__)))
+     dll_path = [curr_path,
++                lib_lightgbm_path,
+                 os.path.join(curr_path, '../../'),
+                 os.path.join(curr_path, 'compile'),
+                 os.path.join(curr_path, '../compile'),
+diff --git a/python-package/setup.py b/python-package/setup.py
+index ee98b1a..2f7ce38 100644
+--- a/python-package/setup.py
++++ b/python-package/setup.py
+@@ -231,7 +231,7 @@ class CustomInstall(install):
+         self.opencl_library = None
+         self.mpi = 0
+         self.hdfs = 0
+-        self.precompile = 0
++        self.precompile = 1
+         self.nomp = 0
+         self.bit32 = 0
+ 
+@@ -274,7 +274,7 @@ class CustomBdistWheel(bdist_wheel):
+         self.opencl_library = None
+         self.mpi = 0
+         self.hdfs = 0
+-        self.precompile = 0
++        self.precompile = 1
+         self.nomp = 0
+         self.bit32 = 0
+ 
+@@ -324,7 +324,10 @@ if __name__ == "__main__":
+         copy_file(os.path.join(CURRENT_DIR, os.path.pardir, 'VERSION.txt'),
+                   os.path.join(CURRENT_DIR, 'lightgbm', 'VERSION.txt'),
+                   verbose=0)  # type:ignore
+-    version = open(os.path.join(CURRENT_DIR, 'lightgbm', 'VERSION.txt'), encoding='utf-8').read().strip()
++
++    # This variable will be set during substitution.
++    version = ''
++
+     readme = open(os.path.join(CURRENT_DIR, 'README.rst'), encoding='utf-8').read()
+ 
+     sys.path.insert(0, CURRENT_DIR)
+@@ -355,7 +358,8 @@ if __name__ == "__main__":
+           zip_safe=False,
+           cmdclass={
+               'install': CustomInstall,
+-              'install_lib': CustomInstallLib,
++              # Lib will be loaded from the lightgbm package.
++              # 'install_lib': CustomInstallLib,
+               'bdist_wheel': CustomBdistWheel,
+               'sdist': CustomSdist,
+           },
+-- 
+2.31.1
+
diff --git a/gnu/packages/patches/lightgbm-use-system-libraries.patch b/gnu/packages/patches/lightgbm-use-system-libraries.patch
new file mode 100644
index 0000000000..115ca02775
--- /dev/null
+++ b/gnu/packages/patches/lightgbm-use-system-libraries.patch
@@ -0,0 +1,58 @@
+From 894648291b9629d51785e4fd1cae820d2858e039 Mon Sep 17 00:00:00 2001
+From: Vinicius Monego <monego@posteo.net>
+Date: Mon, 31 May 2021 21:23:52 -0300
+Subject: [PATCH] Use system libraries.
+
+---
+ CMakeLists.txt                  | 11 ++++++++---
+ include/LightGBM/utils/common.h |  4 ++--
+ 2 files changed, 10 insertions(+), 5 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index b845f36..560e477 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -93,9 +93,6 @@ if(USE_SWIG)
+   endif()
+ endif(USE_SWIG)
+ 
+-SET(EIGEN_DIR "${PROJECT_SOURCE_DIR}/external_libs/eigen")
+-include_directories(${EIGEN_DIR})
+-
+ # See https://gitlab.com/libeigen/eigen/-/blob/master/COPYING.README
+ ADD_DEFINITIONS(-DEIGEN_MPL2_ONLY)
+ 
+@@ -399,6 +396,14 @@ if(USE_SWIG)
+   endif()
+ endif(USE_SWIG)
+ 
++find_package (Eigen3 3.3 REQUIRED NO_MODULE)
++TARGET_LINK_LIBRARIES (lightgbm Eigen3::Eigen)
++TARGET_LINK_LIBRARIES (_lightgbm Eigen3::Eigen)
++
++find_package(fmt)
++TARGET_LINK_LIBRARIES(lightgbm fmt::fmt)
++TARGET_LINK_LIBRARIES(_lightgbm fmt::fmt)
++
+ if(USE_MPI)
+   TARGET_LINK_LIBRARIES(lightgbm ${MPI_CXX_LIBRARIES})
+   TARGET_LINK_LIBRARIES(_lightgbm ${MPI_CXX_LIBRARIES})
+diff --git a/include/LightGBM/utils/common.h b/include/LightGBM/utils/common.h
+index 4357357..00101a5 100644
+--- a/include/LightGBM/utils/common.h
++++ b/include/LightGBM/utils/common.h
+@@ -32,9 +32,9 @@
+ 
+ #if (!((defined(sun) || defined(__sun)) && (defined(__SVR4) || defined(__svr4__))))
+ #define FMT_HEADER_ONLY
+-#include "../../../external_libs/fmt/include/fmt/format.h"
++#include "fmt/format.h"
+ #endif
+-#include "../../../external_libs/fast_double_parser/include/fast_double_parser.h"
++#include "fast_double_parser.h"
+ 
+ #ifdef _MSC_VER
+ #include <intrin.h>
+-- 
+2.31.1
+
