In 1642 he began his wanderings with a visit to England in search of manuscripts of the classics but met with little courtesy from the English scholars.
His health restored, he set out once more in search of codices, passing through Leuven, Brussels, Mechelen, Antwerp and so back to Leiden, everywhere collating manuscripts and taking philological and textual notes.
After studying the classical texts he could obtain, he traveled in 1646 southwards visited on the way Lyon, Marseille, Pisa, Florence (where he paused to publish a new edition of Ovid) and Rome.
The quarrel became both highly personal and widely known, and Heinsius as university librarian refused him access to the books he wished to consult.
Heinsius had two illegitimate children by Margareta Wullen, daughter of a Lutheran minister from Stockholm, who was a nude model in Amsterdam.
He married her only after a lawsuit, but did not want to recognise his sons, Daniel and Nicolaas Heinsius the Younger (1655–1718) but was eventually forced to do so.
He later returned to Holland and was the author of the Den vermakelyken avanturier, ofte De Wispelturige, en niet min Wonderlyke Levens-Loop van Mirandor (The Jolly Adventurer or the Unpredictable and not less Wonderful Life of Mirandor) (1695), the only Dutch-language romance novel of the 17th century.