Café counters across Portugal run on a set of short, specific order words, and getting them slightly wrong doesn't ruin your morning — staff are used to visitors pointing and guessing — but knowing the actual terms means you get what you meant to order the first time, and understand what's written on a menu that has no English translation.
The espresso family
The base order in most of the country is a small, strong espresso shot. In Lisbon this is called a bica; in Porto and the north, the same drink is more often just café. Both refer to the same style of shot, and either word works anywhere in the country — a Lisbon café will understand café, and a Porto café will generally understand bica, even if bica is the more regionally specific term.
If you want that shot with a small splash of milk rather than black, ask for a garoto — literally "little boy," and it comes in a small cup, not a full milk coffee. It's a middle option between a straight bica and a full milky coffee, useful if you find espresso too intense first thing but don't want a large drink.
The milk coffee family: cup or glass
This is where visitors most often order the wrong thing without realizing it, because the two most common milk coffees differ mainly by the vessel they're served in, and that vessel isn't cosmetic — it changes the ratio of coffee to milk.
A meia de leite ("half milk") is served in a cup, roughly the size of a cappuccino, and is closer to a classic coffee-with-milk in proportion — more coffee relative to milk than what follows.
A galão is served in a tall glass, and carries proportionally more steamed milk to a smaller amount of coffee, closer to what a latte drinker abroad would expect. Ask for a galão if you want a larger, milkier drink you can sit with; ask for a meia de leite if you want something closer to a stronger flat white in a normal-sized cup.
Both are ordered simply by name — "um galão, por favor" or "uma meia de leite, por favor" — with no further modifiers usually necessary, since Portuguese cafés generally don't run the extensive size and syrup customization common at chain coffee shops abroad.
Decaf, and other common modifiers
Decaffeinated coffee is descafeinado, and asking for a "bica descafeinada" or "galão descafeinado" is understood everywhere, though smaller, traditional cafés sometimes only stock instant decaf rather than a decaffeinated espresso — worth asking if it matters to you.
Iced coffee is less standardized across Portuguese cafés than in many countries; some serve a mazagran (a sweetened iced black coffee, sometimes with a lemon slice) rather than an iced version of a milk coffee, so don't assume a cold coffee order will map onto what you'd get at home.
The pastel de nata question
The Portuguese custard tart known internationally as pastel de nata is sold at bakeries, cafés and supermarkets across the entire country, made to broadly similar recipes by hundreds of different producers, and ordering "um pastel de nata, por favor" anywhere will get you a version of this tart.
Pastéis de Belém is a different, more specific thing: a single bakery next to the Jerónimos Monastery in the Belém district of Lisbon, footsteps from Belém's discovery monuments. According to the bakery's own history page, its pastries trace back to the early nineteenth century, when clergy displaced by Portugal's 1834 closure of religious orders began selling sweets from a shop next to the monastery, and the bakery states that it has produced its tarts since 1837 "following the ancient 'secret recipe' from the monastery," known only to the pastry chefs who work in what it calls its "secret room." The bakery uses the trademarked name Pastéis de Belém specifically for tarts made in that shop, distinguishing them from the generic pastel de nata sold elsewhere.
What this guide does not cover
This article covers ordering terms, not where to eat or which bakery makes the best pastel de nata — that's a matter of taste this guide isn't set up to judge for you. If a menu uses regional terms this guide doesn't cover, ask the person behind the counter; most Lisbon cafés are used to explaining their own menu to visitors.