We found the pastelaria Zarzuela (pastry & Restaurat) which offers glúten free and also lactose free etc products. We stayed one week in Lisbon and went there 6 times. There are certified by the Portuguese Celiac Associaton.
We tried several delicous products: glúten free muesli for the breakfast as well as fresh glúten free bread. Several times we had the hamburgers and typical Portuguese a la carte dishes. They have about 10 different pastries each day, a lot to choose. Try the almond/chocolate tarte, the éclair or the muffins. Delicious. The have glúten and sugar free ice cream. We ate waffles with ice and fruits all glúten free. It's been years since we've had this.
They are located down town (the baixa) from Lisbon, between the Praça do comerico and the Cais Sodre, at the route from the electrics, the rua do Arsenal. Easy to find.
I am gluten free, and my wife has lactose problems. But we didn't have any problems. So we went there 6 times. Try it.