One of his most well-known books is Comparative Indo-European Linguistics: An Introduction, a standard handbook on Proto-Indo-European that treats the area of linguistic reconstruction thoroughly but also features cultural reconstruction and comparative linguistic methods in general.

Beekes was also a co-author, with L. Bouke van der Meer, of De Etrusken spreken (1991). He advocated the Asia Minor theory to explain the Etruscans' origin.^[2] In 1993, he was elected member of the Royal Netherlands Academy of Arts and Sciences.^[3]

He also did work on Pre-Greek, the (non-Indo-European) language that was spoken in Greece before Greek, possibly around 2000 BC. Since this language was not written, Beekes obtained his information from many words in Classical Greek that show a non-Greek structure and development.^[4]

• The Development of the Proto-Indo-European Laryngeals in Greek. The Hague–Paris: Mouton, 1969.
• The Origins of the Indo-European Nominal Inflection. Innsbruck: IBS, 1985.
• A Grammar of Gatha-Avestan. Leiden: Brill, 1988.
• Vergelijkende taalwetenschap. Een inleiding in de vergelijkende Indo-europese taalwetenschap. Amsterdam: Het Spectrum, 1990.
  • English translation: Comparative Indo-European Linguistics: An Introduction, trans. UvA Vertalers & Paul Gabriner. Amsterdam: Benjamins, 1995; second edition revised and corrected by Michiel de Vaan, 2011.
• with L. Bouke van der Meer, De Etrusken spreken. Muiderberg: Coutinho, 1991.
• The Origin of the Etruscans. Amsterdam: Koninklijke Nederlandse Akademie van Wetenschappen, 2003.
• Etymological Dictionary of Greek, 2 vols. Leiden: Brill, 2009.
• Pre-Greek: Phonology, Morphology, Lexicon, Leiden: Brill, 2014. (Edited by Stefan Norbruis. Translated in Greek.)

• Rekonstruktion und relative Chronologie. Akten der VIII. Fachtagung der Indogermanischen Gesellschaft, Leiden, 31. August – 4. September 1987, ed. Robert S. P. Beekes. Innsbruck: Institut für Sprachwissenschaft, 1992.^{[citation needed]}

• "Mṓnukhes híppoi", Orbis 20 (1971): 138–142.
• "H₂O", Die Sprache 18 (1972): 11–31.
• "The nominative of the hysterodynamic noun-inflection", Zeitschrift für vergleichende Sprachforschung 86 (1972): 30–63.
• "The proterodynamic perfect", Zeitschrift für vergleichende Sprachforschung 87 (1973): 86–98.
• "Two notes on PIE stems in dentals", Historische Grammatik des Griechischen: Laut- und Formenlehre, ed. Helmut Rix. Darmstadt: 1975, pp. 9–14.
• "Intervocalic laryngeal in Gatha-Avestan", Bono Homini Donum: Essays in Historical Linguistics, in Memory of J. Alexander Kerns, eds. Yoël L. Arbeitman & Allan R. Bomhard. Amsterdam: John Benjamins, 1981, pp. 47–64.
• "The disyllabic reduplication of the Sanskrit intensives", Münchener Studien zur Sprachwissenschaft 40 (1981): 19–25.
• "The subjunctive endings of Indo-Iranian", Indo-Iranian Journal 23 (1981): 21–27
• "GAv. må, the PIE word for 'moon, month', and the perfect participle", Journal of Indo-European Studies 10 (1982): 53–64.
• "On laryngeals and pronouns", Zeitschrift für vergleichende Sprachforschung 96 (1983): 200–232.
• "PIE 'sun'", Münchener Studien zur Sprachwissenschaft 43 (1984): 5–8.
• "On Indo-European 'wine'", Münchener Studien zur Sprachwissenschaft 80 (1987): 21–6.
• "The origin of the PIE pronominal inflection", A Festschrift in honour of E. C. Polomé, eds. M. A. Jazayery & W. Winter. NY: de Gruyter, 1987, pp. 73–88.
• "The word for 'four' in PIE", Journal of Indo-European Studies 15 (1987): 215–19.
• "Laryngeal developments: A survey", Die Laryngaltheorie und die Rekonstruktion des indogermanischen Laut- und Formensystems, ed. Alfred Bammesberger. Heidelberg: Carl Winter, 1988, pp. 59–105.
• "PIE RHC – in Greek and other languages", Indogermanische Forschungen 93 (1988): 22–45.
• "The genitive singular of the pronoun in Germanic and Indo-European", Beiträge zur Geschichte der deutschen Sprache und Literatur 110 (1988): 1–5.
• "The nature of the PIE laryngeals", The New Sound of Indo-European: Essays in Phonological Reconstruction, ed. Theo Vennemann. Berlin/NY: de Gruyter, 1989, pp. 23–33.
• "Bloem en blad", 100 jaar etymologisch woordenboek van het Nederlands, eds. A. Moerdijk et al. The Hague: 1990, pp. 375–382.
• "De verwantschap van het Etruskisch", Lampas 23 (1990): 5–18.
• "The genitive in *-osio", Folia linguistica historica 11 (1990): 21–6.
• "The historical grammar of Greek", Linguistic Change and Reconstruction Methodology, ed. P. Baldi. Berlin–NY: de Gruyter, 1990, pp. 305–329.
• "Wackernagel's explanation of the lengthened grade", Sprachwissenschaft und Philologie, eds. H. Eichner & Helmut Rix. Wiesbaden: 1990, pp. 33–53
• "Who were the laryngeals?", In honorem Holger Pedersen: Kolloquium der indogermanischen Gesellschaft vom 25. bis 28. März 1993 in Kopenhagen, ed. J. Rasmussen. Wiesbaden: Ludwig Reichert Verlag 1994, pp. 449–454.
• "Hades and Elysion", Mír Curad. Studies in honor of Calvert Watkins, ed. Jay Jasanoff. Innsbruck: 1998, pp. 17–28.
• "European substratum words in Greek", 125 Jahre Indogermanistik in Graz, eds. Michaela Ofitsch & Christian Zinko. Graz: 2000, pp. 21–31.
• "Indo-European or substrate? φάτνη and κῆρυξ", Languages in Prehistoric Europe, eds. Alfred Bammesberger & Theo Vennemann. Heidelberg: 2003, pp. 109–116.
• "Armenian gišer and the Indo-European word for 'evening'", Per aspera ad asteriscos: Studia Indogermanica in honorem Iens Elmegård Rasmussen sexagenarii. Idibus Martiis anno MMIV, eds. Adam Hyllested et al. Innsbruck: 2004, pp. 59–61.
• "Palatalized consonants in Pre-Greek", Evidence and counter-evidence: essays in honour of Frederik Kortlandt, eds. Alexander Lubotsky et al. Amsterdam: 2008, pp. 45–56.
• Supervisor with Alexander Lubotsky of the Indo-European Etymological Dictionary, 1991 ff.

• Robert S. P. Beekes Memorial website