According to this page on the CP/Portuguese railways site,
http://www.cp.pt/cp/displayPage.do?vgnextoid=e15cf9e12a584010VgnVCM1000007b01a8c0RCRD#8
Bicycles can be transported on Alfa-Pendular and Inter-City trains provided they can be dismantled and stored in the baggage racks or under the passengers seat.
To be honest, I have never seen any one taking a bike on one of these trains.
