The family-owned company, based in Tranent, East Lothian, supplies grain and barley to the Scottish whisky industry and has benefited from soaring demand for the spirit.
According to accounts filed at Companies House, WN Lindsay also saw its costs of sales rise from £76.9m to £100.6m in the 12 months to May 31, 2012.
During the year, it sold its small stevedoring arm to Berwick Harbour Commission for £218,240.
In the accounts, the directors said: "The agricultural sector remains in good health with strong demand for consumers for all cereals.
"The coming year will be challenging due to poor grain yields but opportunities will arise and we will be in a good position to take advantage of these."
Average group staff numbers dipped from 51 to 46 with part of that attributable to the stevedoring sale.
Total employee costs increased from £2.38m to £2.44m.
Directors' emoluments went up from £728,538 to £760,829, with the highest paid seeing a small decline to £154,389, although their pension contributions soared from £5149 to £105,277.
Dividends payments were steady at £225,000, while net debt was cut from £3.8m to £1.5m.
William N Lindsay formed the business in the Leith area of Edinburgh in 1864 and it was based there until 1981 when the head office moved to East Lothian.
The company remains under family ownership, with the fifth generation of Lindsays now working in the business.