Try this.

$users = User::with('services')
                   ->whereHas('services', function($q) {
                       $q->where('active', '=', 1); 
                   })
                   ->orderBy('created_at', 'desc')
                   ->get();

Thanks! Sadly that gives me the same error I was originally hitting,

SQLSTATE[23000]: Integrity constraint violation: 1052 Column 'active' in where clause is ambiguous

That nailed it! I thought I tried something like that earlier but I guess either not or I had something else wrong...

Many thanks

$q->wherePivot('active', 1);

is a more proper way to do it. wherePivot() and orWherePivot() methods are introduced with L4.1.