In the late 1990s it became impossible to export into Russia due to its internal crises, though it had been the principal sales outlet for the Estonian agricultural produce during the Soviet era. Joining the European Union was good for Estonian agriculture, because from then on it was possible to sell food products to other European countries, as there were no longer any customs or importation restrictions, and the Russian market opened up again, too. Estonian farmers began receiving various grants that are still significantly smaller than in western Europe, although manufacturing costs have risen to almost the same level.
Astumine Euroopa Liitu mõjus Eesti põllumajandusele hästi, kuna sellest alates sai müüa toidukaupu teistesse Euroopa riikidesse, sest kadusid tollid ja sisseveopiirangud, ning taasavanes ka Venemaa turg. Eesti põllumehed hakkasid saama erinevaid toetusi, mis on aga endiselt oluliselt väiksemad Lääne-Euroopa omadest, kuigi tootmiskulud on tõusnud peaaegu samale tasemele.Viimaste aastatega on Eesti põllumajandusettevõtted muutunud suuremaks ja järjest enam kasutatakse kaasaegseid tehnoloogiaid, endisaegsest tootmisest pole enam midagi järele jäänud.