public class SQLiteDbContext : DbContext, IUnitOfWork
    {
        public SQLiteDbContext(DbContextOptions options) : base(options)
        { }

        public virtual DbSet<User> Users { set; get; }

namespace EFCoreMultipleDb.DataLayer.SQLite.Context
{
    public class SQLiteDbContextFactory : IDesignTimeDbContextFactory<SQLiteDbContext>
    {
        public SQLiteDbContext CreateDbContext(string[] args)
        {
            var basePath = Directory.GetCurrentDirectory();
            Console.WriteLine($"Using `{basePath}` as the BasePath");
            var configuration = new ConfigurationBuilder()
                                    .SetBasePath(basePath)
                                    .AddJsonFile("appsettings.json")
                                    .Build();
            var builder = new DbContextOptionsBuilder<SQLiteDbContext>();
            var connectionString = configuration.GetConnectionString("SqliteConnection")
                                                .Replace("|DataDirectory|", Path.Combine(basePath, "wwwroot", "app_data"));
            builder.UseSqlite(connectionString);
            return new SQLiteDbContext(builder.Options);
        }
    }
}

{
  "Logging": {
    "LogLevel": {
      "Default": "Warning"
    }
  },
  "AllowedHosts": "*",
  "ConnectionStrings": {
    "SqlServerConnection": "Data Source=(LocalDB)\\MSSQLLocalDB;Initial Catalog=ASPNETCoreSqlDB;AttachDbFilename=|DataDirectory|\\ASPNETCoreSqlDB.mdf;Integrated Security=True;MultipleActiveResultSets=True;",
    "SqliteConnection": "Data Source=|DataDirectory|\\ASPNETCoreSqliteDB.sqlite",
    "InUseKey": "SqliteConnection"
  }
}

var connectionStringKey = Configuration.GetConnectionString("InUseKey");
var connectionString = Configuration.GetConnectionString(connectionStringKey)
                     .Replace("|DataDirectory|", Path.Combine(Directory.GetCurrentDirectory(), "wwwroot", "app_data"));

For /f "tokens=2-4 delims=/ " %%a in ('date /t') do (set mydate=%%c_%%a_%%b)
For /f "tokens=1-2 delims=/:" %%a in ("%TIME: =0%") do (set mytime=%%a%%b)
dotnet build
dotnet ef migrations --startup-project ../EFCoreMultipleDb.Web/ add V%mydate%_%mytime% --context SQLiteDbContext

dotnet build
dotnet ef --startup-project ../EFCoreMultipleDb.Web/ database update --context SQLServerDbContext

namespace EFCoreMultipleDb.Web
{
    public class Startup
    {
        public void Configure(IApplicationBuilder app, IHostingEnvironment env)
        {
            applyPendingMigrations(app);
// ...
        }

        private static void applyPendingMigrations(IApplicationBuilder app)
        {
            var scopeFactory = app.ApplicationServices.GetRequiredService<IServiceScopeFactory>();
            using (var scope = scopeFactory.CreateScope())
            {
                var uow = scope.ServiceProvider.GetService<IUnitOfWork>();
                uow.Migrate();
            }
        }
    }
}

namespace EFCoreMultipleDb.DataLayer.SQLite.Context
{
    public class SQLiteDbContext : DbContext, IUnitOfWork
    {
    // ... 

        public void Migrate()
        {
            this.Database.Migrate();
        }
    }
}

namespace EFCoreMultipleDb.Web
{
    public class Startup
    {
        public void ConfigureServices(IServiceCollection services)
        {
            services.AddScoped<IUsersService, UsersService>();

            var connectionStringKey = Configuration.GetConnectionString("InUseKey");
            var connectionString = Configuration.GetConnectionString(connectionStringKey)
                     .Replace("|DataDirectory|", Path.Combine(Directory.GetCurrentDirectory(), "wwwroot", "app_data"));
            switch (connectionStringKey)
            {
                case "SqlServerConnection":
                    services.AddScoped<IUnitOfWork, SQLServerDbContext>();
                    services.AddDbContext<SQLServerDbContext>(options =>
                    {
                        options.UseSqlServer(
                            connectionString,
                            dbOptions =>
                                {
                                    var minutes = (int)TimeSpan.FromMinutes(3).TotalSeconds;
                                    dbOptions.CommandTimeout(minutes);
                                    dbOptions.EnableRetryOnFailure();
                                });
                    });
                    break;
                case "SqliteConnection":
                    services.AddScoped<IUnitOfWork, SQLiteDbContext>();
                    services.AddDbContext<SQLiteDbContext>(options =>
                    {
                        options.UseSqlite(
                            connectionString,
                            dbOptions =>
                                {
                                    var minutes = (int)TimeSpan.FromMinutes(3).TotalSeconds;
                                    dbOptions.CommandTimeout(minutes);
                                });
                    });
                    break;
                default:
                    throw new NotImplementedException($"`{connectionStringKey}` is not defined in `appsettings.json` file.");
            }

            services.AddMvc().SetCompatibilityVersion(CompatibilityVersion.Version_2_2);
        }

{
  "ConnectionStrings": {
    // …
    "InUseKey": "SqlServerConnection"
  }
}

namespace EFCoreMultipleDb.Services
{
    public interface IUsersService
    {
        Task<User> FindUserAsync(int userId);
    }

    public class UsersService : IUsersService
    {
        private readonly IUnitOfWork _uow;
        private readonly DbSet<User> _users;

        public UsersService(IUnitOfWork uow)
        {
            _uow = uow;
            _users = _uow.Set<User>();
        }

        public Task<User> FindUserAsync(int userId)
        {
            return _users.FindAsync(userId);
        }
    }
}

<Project Sdk="Microsoft.NET.Sdk">
  <PropertyGroup>
    <Description>desc.</Description>
    <VersionPrefix>1.0.0</VersionPrefix>
    <Authors>name</Authors>
    <TargetFramework>netstandard1.6</TargetFramework>
    <GenerateDocumentationFile>true</GenerateDocumentationFile>
    <AssemblyName>name</AssemblyName>
    <PackageId>name</PackageId>
    <PackageTags>MVC;aspnetcore</PackageTags>
    <PackageProjectUrl>https://github.com/proj</PackageProjectUrl>
    <PackageLicenseUrl>https://github.com/proj/blob/master/LICENSE.md</PackageLicenseUrl>
    <PackageTargetFallback>$(PackageTargetFallback);dnxcore50</PackageTargetFallback>
    <GenerateAssemblyConfigurationAttribute>false</GenerateAssemblyConfigurationAttribute>
    <GenerateAssemblyCompanyAttribute>false</GenerateAssemblyCompanyAttribute>
    <GenerateAssemblyProductAttribute>false</GenerateAssemblyProductAttribute>
  </PropertyGroup>
  <ItemGroup>
    <PackageReference Include="Microsoft.AspNetCore.Mvc.Core" Version="1.1.2" />
  </ItemGroup>
  <PropertyGroup Condition=" '$(Configuration)' == 'Release' ">
    <PlatformTarget>anycpu</PlatformTarget>
  </PropertyGroup>
  <Target Name="PostcompileScript" AfterTargets="Build">
    <Exec Command="dotnet pack --no-build --configuration $(Configuration)" />
  </Target>
</Project>

  <PropertyGroup>
    <NoWarn>$(NoWarn);1591</NoWarn>
    <GenerateDocumentationFile>true</GenerateDocumentationFile>
  </PropertyGroup>