Seems that I didn’t inspect Preferences attentively enough initially.
Right answer is:
Preferences → Text and margin font style → Size
EDIT:
updating answer according to comments.
In the latest versions of Spyder IDE path to changing font size is:
Tools → Preferences → General → Appearance → Fonts
EDIT2 (since march 2021):
Tools → Preferences → Appearance → Fonts
EDIT3 (since march 2023):
Python → Preferences → Appearance → Fonts