Short answer. From discovery. Article 91 starts the prescriptive period on the day the crime is discovered by the offended party, the authorities or their agents — not necessarily the day it was committed. When discovery happened, and by whom, is itself something to be proved from the record.
What the law says
The period of prescription shall commence to run from the day on which the crime is discovered by the offended party, the authorities or their agents
Revised Penal Code, Article 91 — When Prescription Starts Running. Read the full provision →
The starting point is knowledge, not the act
Article 91 provides that the period of prescription shall commence to run from the day on which the crime is discovered by the offended party, the authorities or their agents. That is a deliberate choice by the Code. Offences that hide themselves — falsified documents, concealed takings, forgeries that surface only when a record is checked — would otherwise be immune simply because the victim had no way of knowing. So a complainant who learns of an offence long after it happened is not automatically out of time, and the mere passage of years is not by itself an answer.
Three sets of eyes, and the earliest one counts
The article names three possible discoverers: the offended party, the authorities, or their agents. It does not require all three, and it does not let a complainant choose. Whichever of them learned of the crime first is the one that starts the clock. This cuts both ways. A person who genuinely did not know may still be within the period even after a long delay, while a person who did know cannot lengthen the period by delaying a complaint, and an offence already known to the authorities is running whatever the private complainant knew.
What counts as discovery is where cases are fought
The article says the period runs from discovery but does not define the word, and that gap is where most real disputes sit. Was a suspicion enough, or was actual knowledge required? Does a public record that the complainant could have checked count as knowledge he already had? These are argued on the facts of the particular case, and nobody can promise how a court will resolve them. What can be said is that the question is decided on evidence of what was known and when, not on how the delay is characterised afterwards.
Build the timeline before anything else
If you think you are close to the edge of a period, the useful work is documentary. Find what fixes the date you learned of the offence: the letter, the statement of account, the annotation on a title, the audit report, the message that first raised it. Note whether any office or officer knew earlier. The same article carries two further rules that move the computation — the period is interrupted by the filing of a complaint or information, and it does not run while the offender is out of the country — so the full calculation needs all three.