diff --git a/bugbug/model.py b/bugbug/model.py
index 08e474b2f9..ed73b955e4 100644
--- a/bugbug/model.py
+++ b/bugbug/model.py
@@ -22,6 +22,7 @@
 from sklearn.feature_extraction.text import TfidfVectorizer
 from sklearn.metrics import precision_recall_fscore_support
 from sklearn.model_selection import cross_validate, train_test_split
+from sklearn.pipeline import Pipeline
 from sklearn.preprocessing import LabelEncoder
 from tabulate import tabulate
 from xgboost import XGBModel
@@ -35,6 +36,27 @@
 logger = logging.getLogger(__name__)
 
 
+def get_transformer_pipeline(pipeline: Pipeline) -> Pipeline:
+    """Create a pipeline that contains only the transformers.
+
+    This will exclude any steps that do not have a transform method, such as a
+    sampler or estimator.
+
+    Args:
+        pipeline: the pipeline to extract the transformers from.
+
+    Returns:
+        a pipeline that contains only the transformers.
+    """
+    return Pipeline(
+        [
+            (name, transformer)
+            for name, transformer in pipeline.steps
+            if hasattr(transformer, "transform")
+        ]
+    )
+
+
 def classification_report_imbalanced_values(
     y_true, y_pred, labels, target_names=None, sample_weight=None, digits=2, alpha=0.1
 ):
@@ -399,8 +421,9 @@ def train(self, importance_cutoff=0.15, limit=None):
 
         feature_names = self.get_human_readable_feature_names()
         if self.calculate_importance and len(feature_names):
-            explainer = shap.TreeExplainer(self.clf)
-            shap_values = explainer.shap_values(X_train)
+            explainer = shap.TreeExplainer(self.clf.named_steps["estimator"])
+            _X_train = get_transformer_pipeline(self.clf).transform(X_train)
+            shap_values = explainer.shap_values(_X_train)
 
             # In the binary case, sometimes shap returns a single shap values matrix.
             if is_binary and not isinstance(shap_values, list):
@@ -413,7 +436,7 @@ def train(self, importance_cutoff=0.15, limit=None):
 
             shap.summary_plot(
                 summary_plot_value,
-                to_array(X_train),
+                to_array(_X_train),
                 feature_names=feature_names,
                 class_names=self.class_names,
                 plot_type=summary_plot_type,
@@ -628,15 +651,16 @@ def classify(
             pred_class = self.le.inverse_transform([pred_class_index])[0]
 
             if background_dataset is None:
-                explainer = shap.TreeExplainer(self.clf)
+                explainer = shap.TreeExplainer(self.clf.named_steps["estimator"])
             else:
                 explainer = shap.TreeExplainer(
-                    self.clf,
+                    self.clf.named_steps["estimator"],
                     to_array(background_dataset(pred_class)),
                     feature_perturbation="interventional",
                 )
 
-            shap_values = explainer.shap_values(to_array(X))
+            _X = get_transformer_pipeline(self.clf).transform(X)
+            shap_values = explainer.shap_values(to_array(_X))
 
             # In the binary case, sometimes shap returns a single shap values matrix.
             if len(classes[0]) == 2 and not isinstance(shap_values, list):
@@ -645,7 +669,7 @@ def classify(
             important_features = self.get_important_features(
                 importance_cutoff, shap_values
             )
-            important_features["values"] = X
+            important_features["values"] = _X
 
             top_indexes = [
                 int(index)
diff --git a/scripts/commit_classifier.py b/scripts/commit_classifier.py
index 7cc130c044..fc8289208d 100644
--- a/scripts/commit_classifier.py
+++ b/scripts/commit_classifier.py
@@ -26,7 +26,7 @@
 from scipy.stats import spearmanr
 
 from bugbug import db, repository, test_scheduling
-from bugbug.model import Model
+from bugbug.model import Model, get_transformer_pipeline
 from bugbug.models.regressor import RegressorModel
 from bugbug.models.testfailure import TestFailureModel
 from bugbug.utils import (
@@ -402,7 +402,10 @@ def load_user(phid):
             )
 
     def generate_feature_importance_data(self, probs, importance):
-        X_shap_values = shap.TreeExplainer(self.model.clf).shap_values(self.X)
+        _X = get_transformer_pipeline(self.clf).transform(self.X)
+        X_shap_values = shap.TreeExplainer(
+            self.clf.named_steps["estimator"]
+        ).shap_values(_X)
 
         pred_class = self.model.le.inverse_transform([probs[0].argmax()])[0]
 
@@ -414,8 +417,8 @@ def generate_feature_importance_data(self, probs, importance):
             value = importance["importances"]["values"][0, int(feature_index)]
 
             shap.summary_plot(
-                X_shap_values[:, int(feature_index)].reshape(self.X.shape[0], 1),
-                self.X[:, int(feature_index)].reshape(self.X.shape[0], 1),
+                X_shap_values[:, int(feature_index)].reshape(_X.shape[0], 1),
+                _X[:, int(feature_index)].reshape(_X.shape[0], 1),
                 feature_names=[""],
                 plot_type="layered_violin",
                 show=False,
@@ -427,7 +430,7 @@ def generate_feature_importance_data(self, probs, importance):
             img.seek(0)
             base64_img = base64.b64encode(img.read()).decode("ascii")
 
-            X = self.X[:, int(feature_index)]
+            X = _X[:, int(feature_index)]
             y = self.y[X != 0]
             X = X[X != 0]
             spearman = spearmanr(X, y)