Does time spent in Portugal on a residence visa count toward the Schengen 90 days?

Two different legal bases are at work, and mixing them up produces both unnecessary panic and genuine overstays.

In Portugal, you are a resident

A national visa, the D7, D8 or D2, and the AIMA residence permit that follows it, authorise you to be in Portugal. Not as a visitor with an allowance, as a person with a title. You can be here 365 days a year. Nothing is counted, and the 90 in 180 rule is simply not the instrument that applies.

What does constrain you is the opposite of a stay limit: an absence limit. A temporary residence permit holder must not be outside Portugal for more than six consecutive months, or more than eight months in total, during each permit period. Break that and you are risking the permit itself at renewal.

Everywhere else, you are a visitor

Your Portuguese permit lets you travel in the Schengen area, but it does not make you resident in Spain or Germany. In the other member states you are a short stay visitor with the ordinary 90 days in any 180 day period.

People who winter somewhere warmer inside Schengen are the ones who get caught. Three months in the Canaries plus six weeks in Italy is over the line, even though you live in Porto.

Before the permit arrives

The days between landing on a residence visa and holding the card are covered by the visa, not by the short stay allowance. The days you spent scouting Portugal before the visa existed were short stay days and they stay on that ledger.

Count only what belongs in it with Leave By Check, and read the worked examples in the Schengen rule guide for Portugal.