Include filter child collection

Disclaimer: I'm the owner of the project Entity Framework Plus

EF+ Query IncludeFilter feature allows filtering related entities.

var item = _Context.Order
           .IncludeFilter(x => x.Inner.Where(y => y.IsDeleted))
           .IncludeFilter(x => x.Inner.Where(y => y.IsDeleted).Select(y => y.first))
           .IncludeFilter(x => x.Inner.Where(y => y.IsDeleted).Select(y => y.second))
           .Where(x => ( !(x.IsDeleted) && (x.IsActive) && 
                 (x.itemid == id))).FirstOrDefault();

Note: You cannot mix Include & IncludeFilter.

Wiki: EF+ Query IncludeFilter

EDIT: Answer sub-question

But we can achieve this using EF only

Yes, under the hood, my library uses a similar solution as projection

var item = _Context.Order.Select(x => new {
                Order = x,
                Inner = x.Inner.Where(y => y.IsDeleted),
                first = x.Inner.Where(y => y.IsDeleted).Select(y => y.first)
                second = x.Inner.Where(y => y.IsDeleted).Select(y => y.second)
            .Where(x => ( !(x.IsDeleted) && (x.IsActive) && (x.itemid == id)))
            .Select(x => x.Order)

Note: Code have not been tested

EDIT: Answer comment

I came across this issue in EF Core. Are you going to implement IncludeFilter also in the EF+Core version

Starting from the v1.10.0, the IncludeFilter is now supported in EF Core 2.x

See: Release Note

EDIT: Answer sub-question

How can I ThenInclude after filtering

We do not have a ThenInclude yet.

So you need to use IncludeFilter again with all filter and navigate through the list or entity you want to include.