diff --git a/dbms/src/Storages/MergeTree/MergeTreeData.cpp b/dbms/src/Storages/MergeTree/MergeTreeData.cpp
index 3801b81530d..c2396e02988 100644
--- a/dbms/src/Storages/MergeTree/MergeTreeData.cpp
+++ b/dbms/src/Storages/MergeTree/MergeTreeData.cpp
@@ -116,6 +116,7 @@ MergeTreeData::MergeTreeData(
     data_parts_by_state_and_info(data_parts_indexes.get<TagByStateAndInfo>())
 {
     setPrimaryKeyAndColumns(order_by_ast_, primary_key_ast_, columns_);
+    setSkipIndexes(indexes_ast_);
 
     /// NOTE: using the same columns list as is read when performing actual merges.
     merging_params.check(getColumns().getAllPhysical());
@@ -189,8 +190,6 @@ MergeTreeData::MergeTreeData(
         throw Exception(
             "MergeTree data format version on disk doesn't support custom partitioning",
             ErrorCodes::METADATA_MISMATCH);
-
-    setSkipIndexes(indexes_ast_);
 }
 
 
@@ -356,27 +355,32 @@ void MergeTreeData::setSkipIndexes(const ASTPtr & indexes_asts, bool only_check)
     {
         return;
     }
+
+    MergeTreeIndexes new_indexes;
+    std::set<String> names;
+    auto index_list = std::dynamic_pointer_cast<ASTExpressionList>(indexes_asts);
+
+    for (const auto &index_ast : index_list->children)
+    {
+        new_indexes.push_back(
+                std::move(MergeTreeIndexFactory::instance().get(
+                        *this,
+                        std::dynamic_pointer_cast<ASTIndexDeclaration>(index_ast),
+                        global_context)));
+
+        if (names.find(new_indexes.back()->name) != names.end())
+        {
+            throw Exception(
+                    "Index with name `" + new_indexes.back()->name + "` already exsists",
+                    ErrorCodes::LOGICAL_ERROR);
+        }
+        names.insert(new_indexes.back()->name);
+    }
+
     if (!only_check)
     {
-        indexes.clear();
-        std::set<String> names;
-        auto index_list = std::dynamic_pointer_cast<ASTExpressionList>(indexes_asts);
-
-        for (const auto &index_ast : index_list->children)
-        {
-            indexes.push_back(
-                    std::move(MergeTreeIndexFactory::instance().get(
-                            *this,
-                            std::dynamic_pointer_cast<ASTIndexDeclaration>(index_ast),
-                            global_context)));
-            if (names.find(indexes.back()->name) != names.end())
-            {
-                throw Exception(
-                        "Index with name `" + indexes.back()->name + "` already exsists",
-                        ErrorCodes::LOGICAL_ERROR);
-            }
-            names.insert(indexes.back()->name);
-        }
+        skip_indexes_ast = indexes_asts;
+        indexes = std::move(new_indexes);
     }
 }
 
@@ -1056,6 +1060,13 @@ void MergeTreeData::checkAlter(const AlterCommands & commands)
             columns_alter_forbidden.insert(col);
     }
 
+    for (auto index : indexes)
+    {
+        /// TODO: some special error telling about "drop index"
+        for (const String & col : index->expr->getRequiredColumns())
+            columns_alter_forbidden.insert(col);
+    }
+
     if (sorting_key_expr)
     {
         for (const ExpressionAction & action : sorting_key_expr->getActions())
@@ -1111,6 +1122,7 @@ void MergeTreeData::checkAlter(const AlterCommands & commands)
     }
 
     setPrimaryKeyAndColumns(new_order_by_ast, new_primary_key_ast, new_columns, /* only_check = */ true);
+    setSkipIndexes(skip_indexes_ast, /* only_check = */ true);
 
     /// Check that type conversions are possible.
     ExpressionActionsPtr unused_expression;
diff --git a/dbms/src/Storages/MergeTree/MergeTreeData.h b/dbms/src/Storages/MergeTree/MergeTreeData.h
index e71ad5fa9d6..70ae8b25c67 100644
--- a/dbms/src/Storages/MergeTree/MergeTreeData.h
+++ b/dbms/src/Storages/MergeTree/MergeTreeData.h
@@ -583,6 +583,7 @@ public:
 
     /// Secondary (data skipping) indexes for MergeTree
     MergeTreeIndexes indexes;
+    ASTPtr skip_indexes_ast;
 
     /// Names of columns for primary key + secondary sorting columns.
     Names sorting_key_columns;
diff --git a/dbms/src/Storages/StorageMergeTree.cpp b/dbms/src/Storages/StorageMergeTree.cpp
index 833b20ab05b..f71a64662a4 100644
--- a/dbms/src/Storages/StorageMergeTree.cpp
+++ b/dbms/src/Storages/StorageMergeTree.cpp
@@ -244,6 +244,7 @@ void StorageMergeTree::alter(
 
     /// Reinitialize primary key because primary key column types might have changed.
     data.setPrimaryKeyAndColumns(new_order_by_ast, new_primary_key_ast, new_columns);
+    data.setSkipIndexes(data.skip_indexes_ast);
 
     for (auto & transaction : transactions)
         transaction->commit();
diff --git a/dbms/src/Storages/StorageReplicatedMergeTree.cpp b/dbms/src/Storages/StorageReplicatedMergeTree.cpp
index f60250d1be5..50b133482b2 100644
--- a/dbms/src/Storages/StorageReplicatedMergeTree.cpp
+++ b/dbms/src/Storages/StorageReplicatedMergeTree.cpp
@@ -461,6 +461,7 @@ void StorageReplicatedMergeTree::setTableStructure(ColumnsDescription new_column
     /// Even if the primary/sorting keys didn't change we must reinitialize it
     /// because primary key column types might have changed.
     data.setPrimaryKeyAndColumns(new_order_by_ast, new_primary_key_ast, new_columns);
+    data.setSkipIndexes(data.skip_indexes_ast);
 }