There is much speculation about Leeuwenhoek's secrets. The microscopes themselves were not secret. He showed them to people all the time. To grind his lenses, he did the same as any other lens grinder, only smaller. The other lens-making methods were no secret; Hooke's Micrographia, detailing the method of making lenses from drops of molten glass, was one of the best selling books of the time.

Yet early in his career, on October 9th, 1676, Leeuwenhoek wrote to the Royal Society:

My method for seeing the very smallest animalcules and minute eels, I do not impart to others; nor how to see very many animalcules at one time. That I keep for myself alone.

Note that he says "method" and "very smallest". This was the letter that made him famous, and he clearly was sharing the new sights with his neighbors in Delft. By the following spring, March 23, 1677 (AB/CL 31), he wrote,

... whenever I wish to show the animalcules to some curious person or other.

This slender hollow glass tube filled with water, I divide again into 25 or 306, or more parts, and then put it before my microscope, by means of two silver or brass springs, which I have attached to it so as to be able to place the glass tube before my microscope in any desired position, and to be able to push it up and down as I think fit.

Amongst other Spectators, I shew'd it to a gentleman in the above mentioned manner who judged, that in 1/30 part of a quantity of water, equalling the bigness of a Millet-seed, he saw more than a thousand living Animals: which when he highly wondred at, he wondred much more, when I said, there were in it two or three kinds of much smaller animals besides, which did not appear to him, and which I could observe by other glasses and other methods, which I still reserve to my self alone.

Nine years later, in 1685, Thomas Molyneux visited Leeuwenhoek at the request of the Royal Society. His account, a letter to the Society's secretary Francis Aston, was read to the Society and recorded in Birch's History. Molyneaux was elected Fellow the following year.

Such were the microscopes, which I saw, and these are they that he shews to the curious that come and visit him: but besides these, he told me that he had another sort, which no man living had looked through setting aside himself; these he reserves for his own private observations wholly, and he assured me they performed far beyond any, that he had shewed me yet, but would not allow me a sight of them, so all I can do is barely to believe, for I can plead no experience in the matter.

Dobell gives these secret methods several pages of guarded speculation (pp. 330-332). Many short biographies of Leeuwenhoek seem to mention the "secrets" as a dash of romantic flair or to portray him as a hopeless amateur too shy to communicate with real scientists.

There's a related question. Leeuwenhoek left hundreds of little microscopes, complete with mounted lenses, as well as many more mounts without lenses and many lenses without mounts. All but a few are now lost, but from Folkes's and Baker's descriptions after his death as well as descriptions from visitors during his life, it seems that van Leeuwenhoek made a microscope for every specimen, or at least those he wrote about. Why?

After he finished, he stored them, two to a box. Of course, with this method, he could refer to them again, he could show them to visitors, and he bequeathed more than two dozen to the Royal Society. But perhaps there was another reason.