What's the origin of the term 'beancounters'?

The most obvious answer as to why accountants are sometimes referenced, disparagingly, as 'beancounters' might involve counting the beads (or beans) on an abacus. But that's not the case.

There are a number of more likely suggested origins of the phrase - but no one seems to know for sure:

Phrases.org
It is likely that the expression wasn't coined in English but is a translation from German.
 The German word 'Erbsenzähler' (Erbsen = beans and zähler = counter) was used in print by Hans Jakob Christoffel von Grimmelshausen in Simplicissimus', 1668, with the same 'pedantic accountant' meaning that we now use.

It is possible that the English usage came from a later and separate coinage, but unlikely.

 The phrase appears in English in Australia soon after the first use in the USA and again this probably ultimately derived from Germany.

An example is found in The Parliamentary Debates of the Australian House of Representatives, 1928:  "It is not a bean counter's bill. There is no attempt to make any savings."

This insinuation that 'bean counters' were penny-pinching accountants who couldn't see the bigger picture chimes in well with the no-nonsense reputation of Australian politicians.

The phrase flourished down under during the 1930/40s before becoming commonplace throughout the English-speaking world later in the 20th century.

 Word detective

"Bean counter" has an interesting history. It seems to have first appeared in the mid-1970s in the U.S., and its original use was simply as a vivid synonym for "accountant," especially one who brooked no nonsense.

 Its first known occurrence in print was in a 1975 Forbes magazine article that referred to "a smart, tightfisted and austere 'bean counter' accountant from rural Kentucky," though we can assume the quotation marks meant the writer had heard the term in use before the date of the article.

In any case, the allusion is clearly to an accountant so dedicated to detail that he or she counts everything, down to the last small, but still important, bean.

By the 1980s, however, most appearances of "bean counter" in the media were taking on a derogatory tone, and "bean counter" is now frequently used to mean a nitpicker who, lost in the numbers, fails to see the "big picture."

WiseGEEK' site has a more graphic analysis that includes:

While an accountant might be asked to perform a thorough inventory of his or her company's assets, only a bean counter would literally count the number of beans contained in the company kitchen's pantry. A financial bean counter may also scrutinize each department's budget to find any form of potential waste, no matter how insignificant or nominal it appears to be.

It is possible that the description was inspired by overzealous kitchen inventory takers who insisted on counting every bean in a bag or every potato in a sack. The act of counting every bean to the exclusion of more important duties would be viewed by many as the ultimate act of micromanagement. Perhaps the term "bean counter" entered the popular vernacular through the commercial or military food industries, where strict inventory controls are common.