diff --git a/CHANGELOG.md b/CHANGELOG.md
index db776cfd8..921fdc1e8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -26,7 +26,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 -
 ### Fixed
 -
--
+- Fix `MeanSegmentEncoderTransform` to work with subset of segments and raise error on new segments ([#1104](https://github.com/tinkoff-ai/etna/pull/1104))
 -
 - Fix `SegmentEncoderTransform` to work with subset of segments and raise error on new segments ([#1103](https://github.com/tinkoff-ai/etna/pull/1103))
 -
diff --git a/etna/transforms/encoders/mean_segment_encoder.py b/etna/transforms/encoders/mean_segment_encoder.py
index 8f518441c..6a05bec3e 100644
--- a/etna/transforms/encoders/mean_segment_encoder.py
+++ b/etna/transforms/encoders/mean_segment_encoder.py
@@ -1,4 +1,7 @@
-import numpy as np
+import reprlib
+from typing import Dict
+from typing import Optional
+
 import pandas as pd
 
 from etna.transforms import Transform
@@ -13,7 +16,7 @@ class MeanSegmentEncoderTransform(Transform, FutureMixin):
 
     def __init__(self):
         self.mean_encoder = MeanTransform(in_column="target", window=-1, out_column="segment_mean")
-        self.global_means: np.ndarray[float] = None
+        self.global_means: Optional[Dict[str, float]] = None
 
     def fit(self, df: pd.DataFrame) -> "MeanSegmentEncoderTransform":
         """
@@ -30,7 +33,9 @@ def fit(self, df: pd.DataFrame) -> "MeanSegmentEncoderTransform":
             Fitted transform
         """
         self.mean_encoder.fit(df)
-        self.global_means = df.loc[:, self.idx[:, "target"]].mean().values
+        mean_values = df.loc[:, self.idx[:, "target"]].mean().to_dict()
+        mean_values = {key[0]: value for key, value in mean_values.items()}
+        self.global_means = mean_values
         return self
 
     def transform(self, df: pd.DataFrame) -> pd.DataFrame:
@@ -46,9 +51,26 @@ def transform(self, df: pd.DataFrame) -> pd.DataFrame:
         -------
         :
             result dataframe
+
+        Raises
+        ------
+        ValueError:
+            If transform isn't fitted.
+        ValueError:
+            If there are segments that weren't present during training.
         """
+        if self.global_means is None:
+            raise ValueError("The transform isn't fitted!")
+
+        segments = df.columns.get_level_values("segment").unique().tolist()
+        new_segments = set(segments) - self.global_means.keys()
+        if len(new_segments) > 0:
+            raise ValueError(
+                f"This transform can't process segments that weren't present on train data: {reprlib.repr(new_segments)}"
+            )
+
         df = self.mean_encoder.transform(df)
-        segment = df.columns.get_level_values("segment").unique()[0]
+        segment = segments[0]
         nan_timestamps = df[df.loc[:, self.idx[segment, "target"]].isna()].index
-        df.loc[nan_timestamps, self.idx[:, "segment_mean"]] = self.global_means
+        df.loc[nan_timestamps, self.idx[:, "segment_mean"]] = [self.global_means[x] for x in segments]
         return df
diff --git a/tests/test_transforms/test_encoders/test_mean_segment_encoder_transform.py b/tests/test_transforms/test_encoders/test_mean_segment_encoder_transform.py
index 0ac9bced2..49da49e4b 100644
--- a/tests/test_transforms/test_encoders/test_mean_segment_encoder_transform.py
+++ b/tests/test_transforms/test_encoders/test_mean_segment_encoder_transform.py
@@ -9,11 +9,11 @@
 from tests.test_transforms.utils import assert_transformation_equals_loaded_original
 
 
-@pytest.mark.parametrize("expected_global_means", ([[3, 30]]))
+@pytest.mark.parametrize("expected_global_means", [{"Moscow": 3, "Omsk": 30}])
 def test_mean_segment_encoder_fit(simple_df, expected_global_means):
     encoder = MeanSegmentEncoderTransform()
     encoder.fit(simple_df)
-    assert (encoder.global_means == expected_global_means).all()
+    assert encoder.global_means == expected_global_means
 
 
 def test_mean_segment_encoder_transform(simple_df, transformed_simple_df):
@@ -22,6 +22,36 @@ def test_mean_segment_encoder_transform(simple_df, transformed_simple_df):
     pd.testing.assert_frame_equal(transformed_df, transformed_simple_df)
 
 
+def test_subset_segments(simple_df):
+    train_df = simple_df
+    test_df = simple_df.loc[:, pd.IndexSlice["Omsk", :]]
+    transform = MeanSegmentEncoderTransform()
+
+    transform.fit(train_df)
+    transformed_test_df = transform.transform(test_df)
+
+    segments = sorted(transformed_test_df.columns.get_level_values("segment").unique())
+    features = sorted(transformed_test_df.columns.get_level_values("feature").unique())
+    assert segments == ["Omsk"]
+    assert features == ["exog", "segment_mean", "target"]
+
+
+def test_not_fitted_error(simple_df):
+    encoder = MeanSegmentEncoderTransform()
+    with pytest.raises(ValueError, match="The transform isn't fitted"):
+        encoder.transform(simple_df)
+
+
+def test_new_segments_error(simple_df):
+    train_df = simple_df.loc[:, pd.IndexSlice["Moscow", :]]
+    test_df = simple_df.loc[:, pd.IndexSlice["Omsk", :]]
+    transform = MeanSegmentEncoderTransform()
+
+    transform.fit(train_df)
+    with pytest.raises(ValueError, match="This transform can't process segments that weren't present on train data"):
+        _ = transform.transform(test_df)
+
+
 @pytest.fixture
 def almost_constant_ts(random_seed) -> TSDataset:
     df_1 = pd.DataFrame.from_dict({"timestamp": pd.date_range("2021-06-01", "2021-07-01", freq="D")})