Here is how I managed to run tenants migrations in productions. They could be a simpler way of doing it, but in case you are still looking for it, this might help you.

1. Start your app in iex> with
   _build/prod/rel/{my_app}/bin/{my_app} start_iex
2. Run ecto migrations by passing tenant_migrations path like the following.

for tenant <- MyApp.Repo.all_tenants do
 # Run the migrations for the tenant
 migrations_path = "/{release_path}/lib/{MyApp}-{version}/priv/repo/tenant_migrations"
 Ecto.Migrator.run(Hr.Repo, migrations_path, :up, all: true, prefix: tenant)
 IO.puts("Migrations completed for tenant: #{tenant}")
end