diff --git a/.kokoro/presubmit/presubmit-doctest-bigframes.cfg b/.kokoro/presubmit/presubmit-doctest-bigframes.cfg
index 7f514f762f3a..c8298623ff9d 100644
--- a/.kokoro/presubmit/presubmit-doctest-bigframes.cfg
+++ b/.kokoro/presubmit/presubmit-doctest-bigframes.cfg
@@ -9,4 +9,10 @@ env_vars: {
 env_vars: {
     key: "GOOGLE_CLOUD_PROJECT"
     value: "bigframes-testing"
+}
+
+# Override the build file to only run for bigframes.
+env_vars: {
+    key: "TRAMPOLINE_BUILD_FILE"
+    value: "github/google-cloud-python/packages/bigframes/scripts/run_doctest.sh"
 }
\ No newline at end of file
diff --git a/packages/bigframes/bigframes/bigquery/_operations/struct.py b/packages/bigframes/bigframes/bigquery/_operations/struct.py
index 580d93b977c0..d26dd53a6f03 100644
--- a/packages/bigframes/bigframes/bigquery/_operations/struct.py
+++ b/packages/bigframes/bigframes/bigquery/_operations/struct.py
@@ -41,6 +41,7 @@ def struct(value: dataframe.DataFrame) -> series.Series:
 
         >>> srs = series.Series([{"version": 1, "project": "pandas"}, {"version": 2, "project": "numpy"},])
         >>> df = srs.struct.explode()
+        >>> df = df[["project", "version"]]  # set the column order to ensure stable output for doctest
         >>> bbq.struct(df)
         0    {'project': 'pandas', 'version': 1}
         1     {'project': 'numpy', 'version': 2}
diff --git a/packages/bigframes/bigframes/session/loader.py b/packages/bigframes/bigframes/session/loader.py
index 960208063105..a07b6fd71ca7 100644
--- a/packages/bigframes/bigframes/session/loader.py
+++ b/packages/bigframes/bigframes/session/loader.py
@@ -54,6 +54,8 @@
 from google.cloud import bigquery_storage_v1
 from google.cloud.bigquery_storage_v1 import (
     types as bq_storage_types,
+)
+from google.cloud.bigquery_storage_v1 import (
     writer as bq_storage_writer,
 )
 
diff --git a/packages/bigframes/noxfile.py b/packages/bigframes/noxfile.py
index 537d417e9145..3b636399fd0c 100644
--- a/packages/bigframes/noxfile.py
+++ b/packages/bigframes/noxfile.py
@@ -392,9 +392,6 @@ def system_noextras(session: nox.sessions.Session):
 @nox.session(python="3.12")
 def doctest(session: nox.sessions.Session):
     """Run the system test suite."""
-    session.skip(
-        "Temporary skip to enable a PR merge. Remove skip as part of closing https://github.com/googleapis/google-cloud-python/issues/16489"
-    )
 
     run_system(
         session=session,
diff --git a/packages/bigframes/scripts/manage_cloud_functions.py b/packages/bigframes/scripts/manage_cloud_functions.py
index ccf588bde7c2..c92be4ebadbf 100644
--- a/packages/bigframes/scripts/manage_cloud_functions.py
+++ b/packages/bigframes/scripts/manage_cloud_functions.py
@@ -67,6 +67,7 @@ def get_bigframes_functions(project, region):
     functions = GCF_CLIENT.list_functions(
         functions_v2.ListFunctionsRequest(parent=parent)
     )
+
     # Filter bigframes created functions
     functions = [
         function
diff --git a/packages/bigframes/scripts/run_doctest.sh b/packages/bigframes/scripts/run_doctest.sh
new file mode 100755
index 000000000000..d5fd7256ece2
--- /dev/null
+++ b/packages/bigframes/scripts/run_doctest.sh
@@ -0,0 +1,49 @@
+#!/bin/bash
+set -eo pipefail
+
+# Disable buffering, so that the logs stream through.
+export PYTHONUNBUFFERED=1
+
+# Assume we are running from the repo root or we need to find it.
+# If this script is in packages/bigframes/scripts/run_doctest.sh,
+# then repo root is 3 levels up.
+export PROJECT_ROOT=$(realpath "$(dirname "${BASH_SOURCE[0]}")/../../..")
+cd "$PROJECT_ROOT"
+
+git config --global --add safe.directory "$(realpath .)"
+
+package_name="bigframes"
+package_path="packages/${package_name}"
+files_to_check="${package_path}"
+
+# Use the IF block to handle the case where KOKORO vars are missing
+# (e.g. local testing)
+if [[ -n "${KOKORO_GITHUB_PULL_REQUEST_TARGET_BRANCH}" && -n "${KOKORO_GITHUB_PULL_REQUEST_COMMIT}" ]]; then
+    echo "checking changes with 'git diff ${KOKORO_GITHUB_PULL_REQUEST_TARGET_BRANCH}...${KOKORO_GITHUB_PULL_REQUEST_COMMIT} -- ${files_to_check}'"
+
+    package_modified=$(git diff "${KOKORO_GITHUB_PULL_REQUEST_TARGET_BRANCH}...${KOKORO_GITHUB_PULL_REQUEST_COMMIT}" -- "${files_to_check}" | wc -l)
+else
+    # If not a PR (like a local run or a different CI trigger), 
+    # we treat it as 0 so it falls through to the "continuous" check.
+    package_modified=0
+fi
+
+# Check if modified OR if it's a continuous build
+if [[ "${package_modified}" -gt 0 || "$KOKORO_BUILD_ARTIFACTS_SUBDIR" == *"continuous"* ]]; then
+    echo "------------------------------------------------------------"
+    echo "Running doctest for: ${package_name}"
+    echo "------------------------------------------------------------"
+    
+    # Ensure credentials are set for system tests in Kokoro
+    if [[ -z "${GOOGLE_APPLICATION_CREDENTIALS}" && -f "${KOKORO_GFILE_DIR}/service-account.json" ]]; then
+        export GOOGLE_APPLICATION_CREDENTIALS="${KOKORO_GFILE_DIR}/service-account.json"
+    fi
+
+    export GOOGLE_CLOUD_PROJECT="bigframes-testing"
+    NOX_SESSION=("cleanup" "doctest")
+
+    cd "${package_path}"
+    python3 -m nox -s "${NOX_SESSION[@]}"
+else
+    echo "No changes in ${package_name} and not a continuous build, skipping."
+fi
\ No newline at end of file
diff --git a/packages/bigframes/tests/system/small/bigquery/test_json.py b/packages/bigframes/tests/system/small/bigquery/test_json.py
index d2ebb73972a6..8e73440a787c 100644
--- a/packages/bigframes/tests/system/small/bigquery/test_json.py
+++ b/packages/bigframes/tests/system/small/bigquery/test_json.py
@@ -12,6 +12,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import json
+
 import geopandas as gpd  # type: ignore
 import pandas as pd
 import pyarrow as pa
@@ -396,8 +398,8 @@ def test_to_json_from_int():
 def test_to_json_from_struct():
     s = bpd.Series(
         [
-            {"version": 1, "project": "pandas"},
-            {"version": 2, "project": "numpy"},
+            {"project": "pandas", "version": 1},
+            {"project": "numpy", "version": 2},
         ]
     )
     assert dtypes.is_struct_like(s.dtype)
@@ -408,7 +410,9 @@ def test_to_json_from_struct():
         dtype=dtypes.JSON_DTYPE,
     )
 
-    pd.testing.assert_series_equal(actual.to_pandas(), expected.to_pandas())
+    actual_json = [json.loads(x) for x in actual.to_pandas()]
+    expected_json = [json.loads(x) for x in expected.to_pandas()]
+    assert actual_json == expected_json
 
 
 def test_to_json_string_from_int():
@@ -421,8 +425,8 @@ def test_to_json_string_from_int():
 def test_to_json_string_from_struct():
     s = bpd.Series(
         [
-            {"version": 1, "project": "pandas"},
-            {"version": 2, "project": "numpy"},
+            {"project": "pandas", "version": 1},
+            {"project": "numpy", "version": 2},
         ]
     )
     assert dtypes.is_struct_like(s.dtype)
@@ -433,7 +437,9 @@ def test_to_json_string_from_struct():
         dtype=dtypes.STRING_DTYPE,
     )
 
-    pd.testing.assert_series_equal(actual.to_pandas(), expected.to_pandas())
+    actual_json = [json.loads(x) for x in actual.to_pandas()]
+    expected_json = [json.loads(x) for x in expected.to_pandas()]
+    assert actual_json == expected_json
 
 
 def test_json_keys():
diff --git a/packages/bigframes/tests/system/small/test_series.py b/packages/bigframes/tests/system/small/test_series.py
index 5de7ce4256f9..0ac8f1eb61e9 100644
--- a/packages/bigframes/tests/system/small/test_series.py
+++ b/packages/bigframes/tests/system/small/test_series.py
@@ -1234,7 +1234,7 @@ def test_divmods_series(scalars_dfs, col_x, col_y, method):
     # BigQuery's mod functions return NUMERIC values for non-INT64 inputs.
     if bf_div_result.dtype == pd.Int64Dtype():
         bigframes.testing.utils.assert_series_equal(
-            pd_div_result, bf_div_result.to_pandas()
+            pd_div_result, bf_div_result.to_pandas(), check_dtype=False
         )
     else:
         bigframes.testing.utils.assert_series_equal(
@@ -1279,7 +1279,7 @@ def test_divmods_scalars(scalars_dfs, col_x, other, method):
     # BigQuery's mod functions return NUMERIC values for non-INT64 inputs.
     if bf_div_result.dtype == pd.Int64Dtype():
         bigframes.testing.utils.assert_series_equal(
-            pd_div_result, bf_div_result.to_pandas()
+            pd_div_result, bf_div_result.to_pandas(), check_dtype=False
         )
     else:
         bigframes.testing.utils.assert_series_equal(