diff --git a/CHANGELOG.md b/CHANGELOG.md
index 093a681de..77d00ac6b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -40,6 +40,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - 
 - Rework validation of `FoldMask` to not fail on tail nans ([#536](https://github.com/etna-team/etna/pull/536))
 - Add parameter `missing_mode` into `R2` and `MedAE` metrics ([#537](https://github.com/etna-team/etna/pull/537))
+- Update `analysis.forecast.plots.plot_metric_per_segment` to handle `None` from metrics ([#540](https://github.com/etna-team/etna/pull/540))
+- 
 - 
 - 
 
diff --git a/etna/analysis/forecast/plots.py b/etna/analysis/forecast/plots.py
index abc046aba..983bf0500 100644
--- a/etna/analysis/forecast/plots.py
+++ b/etna/analysis/forecast/plots.py
@@ -25,6 +25,8 @@
 from statsmodels.graphics.gofplots import qqplot
 from typing_extensions import Literal
 
+from etna.analysis.forecast.utils import _check_metrics_df_empty_segments
+from etna.analysis.forecast.utils import _check_metrics_df_same_folds_for_each_segment
 from etna.analysis.forecast.utils import _prepare_forecast_results
 from etna.analysis.forecast.utils import _select_prediction_intervals_names
 from etna.analysis.forecast.utils import _validate_intersecting_segments
@@ -687,6 +689,11 @@ def plot_metric_per_segment(
 ):
     """Plot barplot with per-segment metrics.
 
+    If for some segment all metric values are missing, it isn't plotted, and the warning is raised.
+
+    If some segments have different set of folds with non-missing metrics,
+    it can lead to incompatible values between folds. The warning is raised in such case.
+
     Parameters
     ----------
     metrics_df:
@@ -715,12 +722,22 @@ def plot_metric_per_segment(
         if ``metric_name`` isn't present in ``metrics_df``
     NotImplementedError:
         unknown ``per_fold_aggregation_mode`` is given
+
+    Warnings
+    --------
+    UserWarning:
+        There are segments without non-missing metric values.
+    UserWarning:
+        Some segments have different set of folds to be aggregated on due to missing values.
     """
     if barplot_params is None:
         barplot_params = {}
 
     aggregation_mode = PerFoldAggregation(per_fold_aggregation_mode)
 
+    _check_metrics_df_empty_segments(metrics_df=metrics_df, metric_name=metric_name)
+    _check_metrics_df_same_folds_for_each_segment(metrics_df=metrics_df, metric_name=metric_name)
+
     plt.figure(figsize=figsize)
 
     if metric_name not in metrics_df.columns:
@@ -728,10 +745,13 @@ def plot_metric_per_segment(
 
     if "fold_number" in metrics_df.columns:
         metrics_dict = (
-            metrics_df.groupby("segment").agg({metric_name: aggregation_mode.get_function()}).to_dict()[metric_name]
+            metrics_df.groupby("segment")
+            .agg({metric_name: aggregation_mode.get_function()})
+            .dropna()
+            .to_dict()[metric_name]
         )
     else:
-        metrics_dict = metrics_df["segment", metric_name].to_dict()[metric_name]
+        metrics_dict = metrics_df[["segment", metric_name]].set_index("segment").dropna().to_dict()[metric_name]
 
     segments = np.array(list(metrics_dict.keys()))
     values = np.array(list(metrics_dict.values()))
diff --git a/etna/analysis/forecast/utils.py b/etna/analysis/forecast/utils.py
index a796eb8c4..e6e6074ed 100644
--- a/etna/analysis/forecast/utils.py
+++ b/etna/analysis/forecast/utils.py
@@ -1,3 +1,4 @@
+import reprlib
 import warnings
 from copy import deepcopy
 from typing import TYPE_CHECKING
@@ -119,3 +120,31 @@ def _validate_intersecting_segments(fold_numbers: pd.Series):
     for fold_info_1, fold_info_2 in zip(fold_info[:-1], fold_info[1:]):
         if fold_info_2["fold_start"] <= fold_info_1["fold_end"]:
             raise ValueError("Folds are intersecting")
+
+
+def _check_metrics_df_empty_segments(metrics_df: pd.DataFrame, metric_name: str) -> None:
+    """Check if there are segments without any non-missing metrics."""
+    df = metrics_df[["segment", metric_name]]
+    initial_segments = set(df["segment"].unique())
+    df = df.dropna(subset=[metric_name])
+    filtered_segments = set(df["segment"].unique())
+
+    if initial_segments != filtered_segments:
+        missing_segments = initial_segments - filtered_segments
+        missing_segments_repr = reprlib.repr(missing_segments)
+        warnings.warn(
+            f"There are segments with all missing metric values, they won't be plotted: {missing_segments_repr}."
+        )
+
+
+def _check_metrics_df_same_folds_for_each_segment(metrics_df: pd.DataFrame, metric_name: str) -> None:
+    """Check if the same set of folds is present for each segment."""
+    if "fold_number" not in metrics_df.columns:
+        return
+
+    df = metrics_df[["segment", "fold_number", metric_name]]
+    # we don't take into account segments without any non-missing metrics, they are handled by other check
+    df = df.dropna(subset=[metric_name])
+    num_unique = df.groupby("segment")["fold_number"].apply(frozenset).nunique()
+    if num_unique > 1:
+        warnings.warn("Some segments have different set of folds to be aggregated on due to missing values.")
diff --git a/tests/test_analysis/test_forecast/test_plots.py b/tests/test_analysis/test_forecast/test_plots.py
index 31f2fb026..d7d9d7942 100644
--- a/tests/test_analysis/test_forecast/test_plots.py
+++ b/tests/test_analysis/test_forecast/test_plots.py
@@ -1,6 +1,7 @@
 import pandas as pd
 import pytest
 
+from etna.analysis import plot_metric_per_segment
 from etna.analysis import plot_residuals
 from etna.analysis.forecast.plots import _get_borders_comparator
 from etna.metrics import MAE
@@ -50,3 +51,64 @@ def test_compare_error(segments_df):
 def test_compare(segments_df, expected):
     comparator = _get_borders_comparator(segment_borders=segments_df)
     assert comparator(name_a="a", name_b="b") == expected
+
+
+@pytest.fixture
+def metrics_df_with_folds() -> pd.DataFrame:
+    df = pd.DataFrame(
+        {
+            "segment": ["segment_0"] * 3 + ["segment_1"] * 3 + ["segment_2"] * 3,
+            "MAE": [1.0, 2.0, 3.0, 2.0, 3.0, 4.0, 3.0, 4.0, 5.0],
+            "MSE": [None, 3.0, 4.0, 3.0, 4.0, 5.0, 5.0, 6.0, 7.0],
+            "MAPE": [None, None, None, 20.0, 30.0, 40.0, 30.0, 40.0, 50.0],
+            "SMAPE": [None, None, None, None, None, None, 50.0, 60.0, 70.0],
+            "RMSE": [None, None, None, None, None, None, None, None, None],
+            "fold_number": [0, 1, 2, 0, 1, 2, 0, 1, 2],
+        }
+    )
+    return df
+
+
+@pytest.fixture
+def metrics_df_no_folds(metrics_df_with_folds) -> pd.DataFrame:
+    df = metrics_df_with_folds
+    df = df.groupby("segment").mean(numeric_only=False).reset_index().drop("fold_number", axis=1)
+    return df
+
+
+@pytest.mark.parametrize(
+    "df_name, metric_name",
+    [
+        ("metrics_df_with_folds", "MAE"),
+        ("metrics_df_no_folds", "MSE"),
+        ("metrics_df_no_folds", "MSE"),
+    ],
+)
+def test_plot_metric_per_segment_ok(df_name, metric_name, request):
+    metrics_df = request.getfixturevalue(df_name)
+    plot_metric_per_segment(metrics_df=metrics_df, metric_name=metric_name)
+
+
+@pytest.mark.parametrize(
+    "df_name, metric_name",
+    [
+        ("metrics_df_with_folds", "MAPE"),
+        ("metrics_df_no_folds", "RMSE"),
+    ],
+)
+def test_plot_metric_per_segment_warning_empty_segments(df_name, metric_name, request):
+    metrics_df = request.getfixturevalue(df_name)
+    with pytest.warns(UserWarning, match="There are segments with all missing metric values"):
+        plot_metric_per_segment(metrics_df=metrics_df, metric_name=metric_name)
+
+
+@pytest.mark.parametrize(
+    "df_name, metric_name",
+    [
+        ("metrics_df_with_folds", "MSE"),
+    ],
+)
+def test_plot_metric_per_segment_warning_non_comparable_segments(df_name, metric_name, request):
+    metrics_df = request.getfixturevalue(df_name)
+    with pytest.warns(UserWarning, match="Some segments have different set of folds to be aggregated on"):
+        plot_metric_per_segment(metrics_df=metrics_df, metric_name=metric_name)