Upgraded to ASP.NET Core 3.1, getting error about System.Text.Json

I have recently upgraded from ASP.NET Core 2.2 to ASP.NET Core 3.1. Locally, everything seems to work ok, but I have issues when deploying to IIS. The error I am receiving in the Event Viewer is

Application: w3wp.exe
CoreCLR Version: 4.700.19.56402
.NET Core Version: 2.2.4
Description: The process was terminated due to an unhandled exception.
Exception Info: System.IO.FileNotFoundException: Could not load file or assembly 'System.Text.Json, Version=4.0.1.0, Culture=neutral, PublicKeyToken=cc7b13ffcd2ddd51'. The system cannot find the file specified.
File name: 'System.Text.Json, Version=4.0.1.0, Culture=neutral, PublicKeyToken=cc7b13ffcd2ddd51'
   at Microsoft.Extensions.Configuration.Json.JsonConfigurationProvider.Load(Stream stream)
   at Microsoft.Extensions.Configuration.FileConfigurationProvider.Load(Boolean reload)
--- End of stack trace from previous location where exception was thrown ---
   at Microsoft.Extensions.Configuration.FileConfigurationProvider.HandleException(ExceptionDispatchInfo info)
   at Microsoft.Extensions.Configuration.FileConfigurationProvider.Load(Boolean reload)
   at Microsoft.Extensions.Configuration.FileConfigurationProvider.Load()
   at Microsoft.Extensions.Configuration.ConfigurationRoot..ctor(IList`1 providers)
   at Microsoft.Extensions.Configuration.ConfigurationBuilder.Build()
   at Microsoft.Extensions.Hosting.HostBuilder.BuildAppConfiguration()
   at Microsoft.Extensions.Hosting.HostBuilder.Build()
   at <AppName>.Program.Main(String[] args)

This is odd because this error message states it is using .NET Core Version 2.2.4. I have installed the .NET Core 3.1 hosting bundle and restarted the server.

I have run through the troubleshooting tips in this post and found:

• When attempting to run the application from the command line (both running dotnet <AppName>.dll and <AppName>.exe , I get exactly the same error as I did in the Event Viewer.
• I have enabled stdoutLog in the web.config. The directory gets created but no log file is written.
• I have enabled the ASP.NET Core Module debug log:

[aspnetcorev2.dll] Resolving hostfxr parameters for application: 'dotnet' arguments: '.\<AppName>.dll' path: 'C:\inetpub\wwwroot\<AppName>\'
[aspnetcorev2.dll] Known dotnet.exe location: ''
[aspnetcorev2.dll] Process path 'dotnet.exe' is dotnet, treating application as portable
[aspnetcorev2.dll] Resolving absolute path to dotnet.exe from 'dotnet.exe'
[aspnetcorev2.dll] Invoking where.exe to find dotnet.exe
[aspnetcorev2.dll] where.exe invocation returned: 'C:\Program Files\dotnet\dotnet.exe
C:\Program Files (x86)\dotnet\dotnet.exe
'
[aspnetcorev2.dll] Current process bitness type detected as isX64=1
[aspnetcorev2.dll] Processing entry 'C:\Program Files\dotnet\dotnet.exe'
[aspnetcorev2.dll] Binary type 6
[aspnetcorev2.dll] Found dotnet.exe via where.exe invocation at 'C:\Program Files\dotnet\dotnet.exe'
[aspnetcorev2.dll] Resolving absolute path to hostfxr.dll from 'C:\Program Files\dotnet\dotnet.exe'
[aspnetcorev2.dll] hostfxr.dll located at 'C:\Program Files\dotnet\host\fxr\3.1.0\hostfxr.dll'
[aspnetcorev2.dll] Converted argument '.\<AppName>.dll' to 'C:\inetpub\wwwroot\<AppName>\.\<AppName>.dll'
[aspnetcorev2.dll] Parsed hostfxr options: dotnet location: 'C:\Program Files\dotnet\dotnet.exe' hostfxr path: 'C:\Program Files\dotnet\host\fxr\3.1.0\hostfxr.dll' arguments:
[aspnetcorev2.dll] Argument[0] = 'C:\Program Files\dotnet\dotnet.exe'
[aspnetcorev2.dll] Argument[1] = 'C:\inetpub\wwwroot\<AppName>\.\<AppName>.dll'
[aspnetcorev2.dll] Loading hostfxr from location C:\Program Files\dotnet\host\fxr\3.1.0\hostfxr.dll
[aspnetcorev2.dll] Canceling standard stream pipe reader
[aspnetcorev2.dll] Loading request handler:  'C:\inetpub\wwwroot\<AppName>\aspnetcorev2_inprocess.dll'
[aspnetcorev2.dll] Creating handler application
[aspnetcorev2_inprocess.dll] Initializing logs for 'C:\inetpub\wwwroot\<AppName>\aspnetcorev2_inprocess.dll'. Process Id: 4100.. File Version: 13.1.19320.0. Description: IIS ASP.NET Core Module V2 Request Handler. Commit: 2b7e994b8a304700a09617ffc5052f0d943bbcba.
[aspnetcorev2_inprocess.dll] Waiting for initialization
[aspnetcorev2_inprocess.dll] Starting in-process worker thread
[aspnetcorev2_inprocess.dll] Resolving hostfxr parameters for application: 'dotnet' arguments: '.\<AppName>.dll' path: 'C:\inetpub\wwwroot\<AppName>\'
[aspnetcorev2_inprocess.dll] Known dotnet.exe location: 'C:\Program Files\dotnet\dotnet.exe'
[aspnetcorev2_inprocess.dll] Process path 'dotnet.exe' is dotnet, treating application as portable
[aspnetcorev2_inprocess.dll] Resolving absolute path to hostfxr.dll from 'C:\Program Files\dotnet\dotnet.exe'
[aspnetcorev2_inprocess.dll] hostfxr.dll located at 'C:\Program Files\dotnet\host\fxr\3.1.0\hostfxr.dll'
[aspnetcorev2_inprocess.dll] Converted argument '.\<AppName>.dll' to 'C:\inetpub\wwwroot\<AppName>\.\<AppName>.dll'
[aspnetcorev2_inprocess.dll] Parsed hostfxr options: dotnet location: 'C:\Program Files\dotnet\dotnet.exe' hostfxr path: 'C:\Program Files\dotnet\host\fxr\3.1.0\hostfxr.dll' arguments:
[aspnetcorev2_inprocess.dll] Argument[0] = 'C:\Program Files\dotnet\dotnet.exe'
[aspnetcorev2_inprocess.dll] Argument[1] = 'C:\inetpub\wwwroot\<AppName>\.\<AppName>.dll'
[aspnetcorev2_inprocess.dll] Setting environment variable ASPNETCORE_IIS_HTTPAUTH=anonymous;
[aspnetcorev2_inprocess.dll] Setting environment variable ASPNETCORE_IIS_PHYSICAL_PATH=C:\inetpub\wwwroot\<AppName>\
[aspnetcorev2_inprocess.dll] Loading hostfxr from location C:\Program Files\dotnet\host\fxr\3.1.0\hostfxr.dll
[aspnetcorev2_inprocess.dll] Initial Dll directory: '', current directory: 'c:\windows\system32\inetsrv'
[aspnetcorev2_inprocess.dll] Setting dll directory to c:\windows\system32\inetsrv
[aspnetcorev2_inprocess.dll] Setting current directory to C:\inetpub\wwwroot\<AppName>\
[aspnetcorev2_inprocess.dll] Event Log: 'Application '/LM/W3SVC/1/ROOT/<AppName>' with physical root 'C:\inetpub\wwwroot\<AppName>\' failed to load coreclr. Exception message:
Error occured when initializing inprocess application, Return code: 0x80008083' 
End Event Log Message.
[aspnetcorev2_inprocess.dll] InvalidOperationException 'Error occured when initializing inprocess application, Return code: 0x80008083' caught at F:\workspace\_work\1\s\src\Servers\IIS\AspNetCoreModuleV2\InProcessRequestHandler\inprocessapplication.cpp:346 
[aspnetcorev2_inprocess.dll] Stopping in-process worker thread
[aspnetcorev2_inprocess.dll] Stopping CLR
[aspnetcorev2_inprocess.dll] Event Log: 'Application '/LM/W3SVC/1/ROOT/<AppName>' with physical root 'C:\inetpub\wwwroot\<AppName>\' failed to load coreclr. Exception message:
CLR worker thread exited prematurely' 
End Event Log Message.
[aspnetcorev2_inprocess.dll] InvalidOperationException 'CLR worker thread exited prematurely' caught at F:\workspace\_work\1\s\src\Servers\IIS\AspNetCoreModuleV2\InProcessRequestHandler\inprocessapplication.cpp:407 
[aspnetcorev2_inprocess.dll] Failed HRESULT returned: 0x8007023e at F:\workspace\_work\1\s\src\Servers\IIS\AspNetCoreModuleV2\InProcessRequestHandler\dllmain.cpp:131 
[aspnetcorev2_inprocess.dll] Starting app_offline monitoring in application 'C:\inetpub\wwwroot\<AppName>\'
[aspnetcorev2_inprocess.dll] Starting file watcher thread

Here is my Program.cs:

public static void Main(string[] args)
{
    Directory.SetCurrentDirectory(Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location));
    XmlDocument log4netConfig = new XmlDocument();
    log4netConfig.Load(File.OpenRead("log4net.config"));
    ILoggerRepository repo = log4net.LogManager.CreateRepository(
        Assembly.GetEntryAssembly(),
        typeof(log4net.Repository.Hierarchy.Hierarchy));
    log4net.Config.XmlConfigurator.Configure(repo, log4netConfig["log4net"]);

    CreateHostBuilder(args).Build().Run();
}

public static IHostBuilder CreateHostBuilder(string[] args) =>
    Host.CreateDefaultBuilder(args)
    .ConfigureWebHostDefaults(webBuilder =>
    {
        webBuilder.UseIIS();
        webBuilder.UseStartup<Startup>();
    });

Here are the important bits of my Startup.cs

public void ConfigureServices(IServiceCollection services)
{
    services.AddOptions();
    services.AddScoped<INotifyService, NotifyService>();
    services.AddControllers().AddNewtonsoftJson();

    // Authentication and CORS settings

    services.AddSignalR().AddNewtonsoftJsonProtocol();
}

public void Configure(IApplicationBuilder app, IWebHostEnvironment env)
{
    app.ConfigureExceptionHandler();

    app.UseRouting();
    app.UseStaticFiles();
    app.UseCors("CorsPolicy");

    app.UseAuthentication();
    app.UseAuthorization();

    app.UseHttpsRedirection();
    app.UseEndpoints(endpoints =>
    {
        endpoints.MapHub<NotifyHub>("/notify");
        endpoints.MapControllerRoute("default", "{controller=Home}/{action=Index}");
    });
    app.UseDefaultFiles();
}

I think the .NET Core Version in the Event Viewer error is key, but I can't work out how to force it to use 3.1.

UPDATE - Add .csproj file information

The relevant parts of my .csproj file are:

<PropertyGroup>
    <TargetFramework>netcoreapp3.1</TargetFramework>
  </PropertyGroup>

  <PropertyGroup>
    <RuntimeFrameworkVersion>3.1.0</RuntimeFrameworkVersion>
    <PlatformTarget>AnyCPU</PlatformTarget>
    <RuntimeIdentifier>win-x64</RuntimeIdentifier>
  </PropertyGroup>

The trick that solves 90% of the issues since Visual Studio 2002 ;-)

manually delete all bin and obj folders in your solution.