You do not apply for EES.
The EU Entry/Exit System (EES) is not a visa and not a pre-trip authorization. It is a border-control registration system for non-EU travelers entering/leaving the Schengen area for short stays. It records your passport data, entry/exit dates, facial image, and fingerprints at the border. (Travel Europe)
For your Portugal/Spain trip, here’s what you do:
Bring your valid passport.
At your first Schengen entry point
—
Lisbon. At the Lisbon Airport — follow airport signs for
non-EU/non-Schengen passport control. Schengen is a group of countries
in the EU that require passport control for non-EU citizens.
Use the EES kiosk or border officer process if directed. You may be asked for:
passport scan
facial photo
fingerprints
short-stay entry questions
There is no EES fee and no online application required before arrival. (GOV.UK)
Allow extra time at border control, especially if this is your first EES registration.
Do not confuse EES with ETIAS. EES is the border registration system. ETIAS is the separate travel authorization that visa-exempt travelers will eventually (late 2026) apply for online before travel, but that is not the same thing as EES. (Travel Europe)
One optional item: some countries/airports may support the EU “Travel to Europe” app for pre-registration of some details, but it is voluntary and does not replace the border check. You can get the app from Apple App Store and Google Play Store. (swedenabroad.se)