diff --git a/include/LightGBM/c_api.h b/include/LightGBM/c_api.h
index b43f096c31ee..8f8137df1f48 100644
--- a/include/LightGBM/c_api.h
+++ b/include/LightGBM/c_api.h
@@ -422,7 +422,7 @@ LIGHTGBM_C_EXPORT int LGBM_DatasetCreateFromMat(const void* data,
  * \param data_type Type of ``data`` pointer, can be ``C_API_DTYPE_FLOAT32`` or ``C_API_DTYPE_FLOAT64``
  * \param nrow Number of rows
  * \param ncol Number of columns
- * \param is_row_major 1 for row-major, 0 for column-major
+ * \param is_row_major Pointer to the data layouts. 1 for row-major, 0 for column-major
  * \param parameters Additional parameters
  * \param reference Used to align bin mapper with other dataset, nullptr means isn't used
  * \param[out] out Created dataset
@@ -433,7 +433,7 @@ LIGHTGBM_C_EXPORT int LGBM_DatasetCreateFromMats(int32_t nmat,
                                                  int data_type,
                                                  int32_t* nrow,
                                                  int32_t ncol,
-                                                 int is_row_major,
+                                                 int* is_row_major,
                                                  const char* parameters,
                                                  const DatasetHandle reference,
                                                  DatasetHandle* out);
diff --git a/python-package/lightgbm/basic.py b/python-package/lightgbm/basic.py
index 7b152fd2b006..5fa3cb872ca7 100644
--- a/python-package/lightgbm/basic.py
+++ b/python-package/lightgbm/basic.py
@@ -2342,6 +2342,7 @@ def __init_from_list_np2d(
             ptr_data = (ctypes.POINTER(ctypes.c_double) * len(mats))()
         else:
             ptr_data = (ctypes.POINTER(ctypes.c_float) * len(mats))()
+        layouts = (ctypes.c_int * len(mats))()
 
         holders = []
         type_ptr_data = -1
@@ -2355,15 +2356,13 @@ def __init_from_list_np2d(
 
             nrow[i] = mat.shape[0]
 
-            if mat.dtype == np.float32 or mat.dtype == np.float64:
-                mats[i] = np.asarray(mat.reshape(mat.size), dtype=mat.dtype)
-            else:  # change non-float data to float data, need to copy
-                mats[i] = np.array(mat.reshape(mat.size), dtype=np.float32)
+            mat, layout = _np2d_to_np1d(mat)
 
-            chunk_ptr_data, chunk_type_ptr_data, holder = _c_float_array(mats[i])
+            chunk_ptr_data, chunk_type_ptr_data, holder = _c_float_array(mat)
             if type_ptr_data != -1 and chunk_type_ptr_data != type_ptr_data:
                 raise ValueError("Input chunks must have same type")
             ptr_data[i] = chunk_ptr_data
+            layouts[i] = layout
             type_ptr_data = chunk_type_ptr_data
             holders.append(holder)
 
@@ -2375,7 +2374,7 @@ def __init_from_list_np2d(
                 ctypes.c_int(type_ptr_data),
                 nrow.ctypes.data_as(ctypes.POINTER(ctypes.c_int32)),
                 ctypes.c_int32(ncol),
-                ctypes.c_int(_C_API_IS_ROW_MAJOR),
+                layouts,
                 _c_str(params_str),
                 ref_dataset,
                 ctypes.byref(self._handle),
diff --git a/src/c_api.cpp b/src/c_api.cpp
index cf6577ad5e2c..967d00d3bd15 100644
--- a/src/c_api.cpp
+++ b/src/c_api.cpp
@@ -1309,7 +1309,7 @@ int LGBM_DatasetCreateFromMat(const void* data,
                                     data_type,
                                     &nrow,
                                     ncol,
-                                    is_row_major,
+                                    &is_row_major,
                                     parameters,
                                     reference,
                                     out);
@@ -1320,7 +1320,7 @@ int LGBM_DatasetCreateFromMats(int32_t nmat,
                                int data_type,
                                int32_t* nrow,
                                int32_t ncol,
-                               int is_row_major,
+                               int* is_row_major,
                                const char* parameters,
                                const DatasetHandle reference,
                                DatasetHandle* out) {
@@ -1337,7 +1337,7 @@ int LGBM_DatasetCreateFromMats(int32_t nmat,
 
   std::vector<std::function<std::vector<double>(int row_idx)>> get_row_fun;
   for (int j = 0; j < nmat; ++j) {
-    get_row_fun.push_back(RowFunctionFromDenseMatric(data[j], nrow[j], ncol, data_type, is_row_major));
+    get_row_fun.push_back(RowFunctionFromDenseMatric(data[j], nrow[j], ncol, data_type, is_row_major[j]));
   }
 
   if (reference == nullptr) {
diff --git a/tests/python_package_test/test_basic.py b/tests/python_package_test/test_basic.py
index bdd4d3f58b80..f34be5cc1574 100644
--- a/tests/python_package_test/test_basic.py
+++ b/tests/python_package_test/test_basic.py
@@ -983,3 +983,17 @@ def test_equal_datasets_from_row_major_and_col_major_data(tmp_path):
 
     # check datasets are equal
     assert filecmp.cmp(ds_row_path, ds_col_path)
+
+
+def test_equal_datasets_from_one_and_several_matrices_w_different_layouts(rng, tmp_path):
+    # several matrices
+    mats = [np.require(rng.random(size=(100, 2)), requirements=order) for order in ("C", "F", "F", "C")]
+    several_path = tmp_path / "several.txt"
+    lgb.Dataset(mats)._dump_text(several_path)
+
+    # one matrix
+    mat = np.vstack(mats)
+    one_path = tmp_path / "one.txt"
+    lgb.Dataset(mat)._dump_text(one_path)
+
+    assert filecmp.cmp(one_path, several_path)