Green and red, obviously. Look a little closer at what's sitting on top of them.
Ask someone to describe the Portuguese flag and you'll get "green and red" almost every time. Two vertical bands, green on the hoist side, red on the fly. That is a fair description of the background and it is not a description of the flag.
Sitting over the join is the national coat of arms: a yellow armillary sphere, a white shield with blue escutcheons inside it, and small white dots arranged within those. Once you count everything actually printed on the cloth, Portugal's flag uses five colours, not two.
You could argue for a rule that ignores emblems and judges only the field. It sounds tidy until you try to apply it. Where does an emblem stop and a design element begin? Is a canton an emblem? A stripe with a pattern woven into it? A crest that covers a third of the flag?
The rule that survives contact with all 190-odd flags is the simplest one: count every colour that appears. A coat of arms brings its own colours with it, and they are as much part of the flag as the background is. That rule needs no exceptions, which is exactly what makes it usable.
Malta's flag is white and red, split vertically. Simple enough. In the upper corner sits the George Cross, awarded to the island for its endurance under bombardment in the Second World War, and it is rendered in grey with a red border. Grey is a third colour, and it is there on the official flag rather than as decoration.
Malta is a good test case because the emblem is small and easy to overlook. The rule doesn't care about size.
A lot of flags are two colours plus a badge. Spain is red and yellow, with a coat of arms carrying half a dozen more. Croatia's red and white chequerboard sits under a crown of five shields, each with its own colouring. Serbia, Slovakia, Montenegro and Moldova all follow the same pattern: a simple tricolour or bicolour, then arms that quietly triple the colour count.
Andorra and Mexico are more dramatic examples. Both are green, white and red vertical bands — already three — and both then add a detailed central emblem. Mexico's eagle, snake and wreath alone contain several distinct colours.
Bolivia, Ecuador, Peru and Guatemala all have state flags that differ from their civil flags purely by the presence of the arms, which is a reminder that many countries fly more than one version of the same design.
San Marino's flag is white and light blue with the national coat of arms in the centre — and the arms are elaborate, with towers, feathers, a crown and a wreath. It comes up because people remember the flag as two calm colours and forget what is drawn on it. The civil version without arms exists, but the state flag is the one that gets flown and pictured.
If a flag looks like two colours in your memory, that is usually a sign the emblem is small — not that it isn't there.