diff --git a/src/Storages/MergeTree/MergeTreeData.cpp b/src/Storages/MergeTree/MergeTreeData.cpp
index 44e81c8d017..3841295b875 100644
--- a/src/Storages/MergeTree/MergeTreeData.cpp
+++ b/src/Storages/MergeTree/MergeTreeData.cpp
@@ -2600,7 +2600,17 @@ void MergeTreeData::checkAlterIsPossible(const AlterCommands & commands, Context
                 }
             }
 
-            dropped_columns.emplace(command.column_name);
+            if (old_metadata.columns.has(command.column_name))
+            {
+                dropped_columns.emplace(command.column_name);
+            }
+            else
+            {
+                const auto & nested = old_metadata.columns.getNested(command.column_name);
+                for (const auto & nested_column : nested)
+                    dropped_columns.emplace(nested_column.name);
+            }
+
         }
         else if (command.type == AlterCommand::RESET_SETTING)
         {
diff --git a/tests/queries/0_stateless/02500_prevent_drop_nested_if_empty_part.reference b/tests/queries/0_stateless/02500_prevent_drop_nested_if_empty_part.reference
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/tests/queries/0_stateless/02500_prevent_drop_nested_if_empty_part.sql b/tests/queries/0_stateless/02500_prevent_drop_nested_if_empty_part.sql
new file mode 100644
index 00000000000..529f574d32d
--- /dev/null
+++ b/tests/queries/0_stateless/02500_prevent_drop_nested_if_empty_part.sql
@@ -0,0 +1,49 @@
+DROP TABLE IF EXISTS 02500_nested;
+
+SET flatten_nested = 1;
+
+CREATE TABLE 02500_nested(arr Array(Tuple(a Int32, b Int32))) Engine=MergeTree ORDER BY tuple();
+INSERT INTO 02500_nested(arr.a, arr.b) VALUES ([1], [2]);
+ALTER TABLE 02500_nested ADD COLUMN z Int32;
+ALTER TABLE 02500_nested DROP COLUMN arr; -- { serverError BAD_ARGUMENTS }
+DROP TABLE 02500_nested;
+
+CREATE TABLE 02500_nested(arr Array(Tuple(a Int32, b Int32)), z Int32) Engine=MergeTree ORDER BY tuple();
+INSERT INTO 02500_nested(arr.a, arr.b, z) VALUES ([1], [2], 2);
+ALTER TABLE 02500_nested DROP COLUMN arr;
+DROP TABLE 02500_nested;
+
+CREATE TABLE 02500_nested(nes Nested(a Int32, b Int32)) Engine=MergeTree ORDER BY tuple();
+INSERT INTO 02500_nested(nes.a, nes.b) VALUES ([1], [2]);
+ALTER TABLE 02500_nested ADD COLUMN z Int32;
+ALTER TABLE 02500_nested DROP COLUMN nes; -- { serverError BAD_ARGUMENTS }
+DROP TABLE 02500_nested;
+
+CREATE TABLE 02500_nested(nes Array(Tuple(a Int32, b Int32)), z Int32) Engine=MergeTree ORDER BY tuple();
+INSERT INTO 02500_nested(nes.a, nes.b, z) VALUES ([1], [2], 2);
+ALTER TABLE 02500_nested DROP COLUMN nes;
+DROP TABLE 02500_nested;
+
+SET flatten_nested = 0;
+
+CREATE TABLE 02500_nested(arr Array(Tuple(a Int32, b Int32))) Engine=MergeTree ORDER BY tuple();
+INSERT INTO 02500_nested(arr) VALUES ([(1, 2)]);
+ALTER TABLE 02500_nested ADD COLUMN z Int32;
+ALTER TABLE 02500_nested DROP COLUMN arr; -- { serverError BAD_ARGUMENTS }
+DROP TABLE 02500_nested;
+
+CREATE TABLE 02500_nested(arr Array(Tuple(a Int32, b Int32)), z Int32) Engine=MergeTree ORDER BY tuple();
+INSERT INTO 02500_nested(arr, z) VALUES ([(1, 2)], 2);
+ALTER TABLE 02500_nested DROP COLUMN arr;
+DROP TABLE 02500_nested;
+
+CREATE TABLE 02500_nested(nes Nested(a Int32, b Int32)) Engine=MergeTree ORDER BY tuple();
+INSERT INTO 02500_nested(nes) VALUES ([(1, 2)]);
+ALTER TABLE 02500_nested ADD COLUMN z Int32;
+ALTER TABLE 02500_nested DROP COLUMN nes; -- { serverError BAD_ARGUMENTS }
+DROP TABLE 02500_nested;
+
+CREATE TABLE 02500_nested(nes Array(Tuple(a Int32, b Int32)), z Int32) Engine=MergeTree ORDER BY tuple();
+INSERT INTO 02500_nested(nes, z) VALUES ([(1, 2)], 2);
+ALTER TABLE 02500_nested DROP COLUMN nes;
+DROP TABLE 02500_nested;