It was straight forward years ago. Not anymore.
1. You go to MIP and ask for new certificado de nacionalidad. The list of documents needed for that is on their website. Will take 10 to 20 days to get it ready.
2. You go to your Oficialia de Estado Civil and get Acto de Nacimiento Validada. If you were naturalized long time ago, ask your Oficialia de Estado Civil to check if they have scanned and uploaded all your documents to the JCE system.
3. You make an appointment at Passport Office on the Malecon. You can't start the process online, just make the appointment.
4 On the day of your appointment, after waiting an hour or so in the long line to enter there, you say that you are naturalized and they tell you to go to the window 16.
5. You go to the window 16 (you will see the sign 'Legal' there) and give all your documents. If it's your first passport, you pay regular fee for 6 years passport. If you had one before, you can apply for 10 years passport and you have to pay for VIP and 10 years, but there will be no VIP for you.
6. They will check your documents in their system, probably will take an hour or so. Then they let you go thru the the standard process (confirming your data, signature and fingerprints in another window, and then wait another hour in a long line to take a photo. After they take your picture, you're done for that day, you go home. They will give you a number at window 16 where you call in a week or two.
7. You call in a week or two, if your passport is approved, it will not be printed anyway until you go there. So you go there early, before 10 AM. Go to the window 16 again (after waiting an hour in the line of course), they tell you to wait. You wait another hour, then they tell you that they have sent your application to print your passport. If you paid for VIP, you have to take a ticket for receiving the passport, but not right away! Wait until 2 PM, then go, because if you do it before, they will say that it's not ready yet, so you will just wait an hour in the line for nothing. So, you return after 2 PM, take the ticket to get the passport, but it will not be ready of course. So there will be 2 or 3 or 4 hours delay, probably it will be printed at 6 PM more or less and you ca receive it. That's if you paid for VIP. If you did not pay for VIP, you don't receive your passport he same day, so after they said OK we have sent it to print it, you can wait something like 6 days, then come back, wait another hour in the line, get your ticket to receive it (if it's ready), then that 3–4–6 hours waiting in a total mess and you get it.