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Yes. Years spent lawfully on a temporary residence permit, including for research, can count toward the five years needed for long-term resident status.
The researcher permit is a temporary residence permit, and lawful time on a temporary permit is what builds your path to Estonia's long-term resident (permanent) status, which requires five years of residence immediately before applying.
To move from research to permanent residence, you will also need to meet the permanent-residence conditions, including B1 Estonian, stable income, and health insurance. Keeping your residence registered and your permits continuous helps protect the qualifying clock.
Get a personalised assessment from a licensed ACME advisor, or ask Acey.