diff --git a/lib/ecto/migration/schema_migration.ex b/lib/ecto/migration/schema_migration.ex
index 93248f7a..1da5944c 100644
--- a/lib/ecto/migration/schema_migration.ex
+++ b/lib/ecto/migration/schema_migration.ex
@@ -12,7 +12,9 @@ defmodule Ecto.Migration.SchemaMigration do
     timestamps updated_at: false
   end
 
-  @opts [timeout: :infinity, log: false]
+  # The migration flag is used to signal to the repository
+  # we are in a migration operation.
+  @opts [timeout: :infinity, log: false, schema_migration: true]
 
   def ensure_schema_migrations_table!(repo, config, opts) do
     {repo, source} = get_repo_and_source(repo, config)
@@ -29,9 +31,9 @@ defmodule Ecto.Migration.SchemaMigration do
     repo.__adapter__().execute_ddl(meta, {:create_if_not_exists, table, commands}, @opts)
   end
 
-  def versions(repo, config) do
+  def versions(repo, config, prefix) do
     {repo, source} = get_repo_and_source(repo, config)
-    {repo, from(m in source, select: type(m.version, :integer))}
+    {repo, from(m in source, select: type(m.version, :integer)), [prefix: prefix] ++ @opts}
   end
 
   def up(repo, config, version, prefix) do
diff --git a/lib/ecto/migrator.ex b/lib/ecto/migrator.ex
index 5b7db841..4c9d41b2 100644
--- a/lib/ecto/migrator.ex
+++ b/lib/ecto/migrator.ex
@@ -500,8 +500,7 @@ defmodule Ecto.Migrator do
         end
       end
 
-      all_opts = [prefix: opts[:prefix], timeout: :infinity, log: false]
-      {migration_repo, query} = SchemaMigration.versions(repo, config)
+      {migration_repo, query, all_opts} = SchemaMigration.versions(repo, config, opts[:prefix])
 
       result =
         if should_lock? do
diff --git a/test/test_repo.exs b/test/test_repo.exs
index 05713330..cc2b34f2 100644
--- a/test/test_repo.exs
+++ b/test/test_repo.exs
@@ -32,16 +32,19 @@ defmodule EctoSQL.TestAdapter do
 
   # Migration emulation
 
-  def execute(_, _, {:nocache, {:all, %{from: %{source: {"schema_migrations", _}}}}}, _, _) do
+  def execute(_, _, {:nocache, {:all, %{from: %{source: {"schema_migrations", _}}}}}, _, opts) do
+    true = opts[:schema_migration]
     {length(migrated_versions()), Enum.map(migrated_versions(), &[elem(&1, 0)])}
   end
 
   def execute(_, _meta, {:nocache, {:delete_all, %{from: %{source: {"schema_migrations", _}}}}}, [version], opts) do
+    true = opts[:schema_migration]
     Process.put(:migrated_versions, List.delete(migrated_versions(), {version, opts[:prefix]}))
     {1, nil}
   end
 
   def insert(_, %{source: "schema_migrations"}, val, _, _, opts) do
+    true = opts[:schema_migration]
     version = Keyword.fetch!(val, :version)
     Process.put(:migrated_versions, [{version, opts[:prefix]} | migrated_versions()])
     {:ok, []}