Both are residency permits granted in Spain by the UGE, so the difference is what each one lets you do rather than how you file. The Startup residency permit runs 3 years, sets no monthly income threshold — you show savings of €34,188 (2026) instead — covers your family, and lets you build a company in Spain and hire. The Digital Nomad residency permit (also up to 3 years when filed from Spain via the UGE) asks for proof of about €2,849/month and is built for remote work for clients or employers outside Spain, which limits local business activity.
The wait differs too, and ENISA is why. For the Digital Nomad residency permit the legal deadline is 20 working days, about 4 weeks. The Startup residency permit takes about 8 weeks in practice, because the UGE stops that clock while ENISA reports on the business plan. Both are lawful residence, so both count towards permanent residence and citizenship. If you are building a company here, the Startup residency permit fits; if you are working remotely for others, the Digital Nomad residency permit usually does.