​When the crop stage and weather conditions are favourable, harvest can begin! Both mechanical and hand-harvesting methods are used to harvest crop research plots.  In very early breeding generations, single plants are often taken from the most-promising varieties to be grown in the next generation. Often, these early generations are grown in single rows instead of plots, making mechanical harvest more difficult as most plot combines are designed to take up entire plots instead of single rows.  In situations where a plot combine is not feasible or available, plants are often hand harvested using sickles or knives. Afterwards the harvested plants will be threshed in the field or put into bags and threshed later. Hand-harvesting is an effective, and often necessary, method for harvesting research trials, however, it is quite time-consuming and requires a large labour force.

In later stages of breeding research, or research programs in which the plants are grown in typical plot formations, plot combines can be used. These combines are relatively small and are only as wide as the research plots. Each plot is harvested separately to allow for complete isolation of the grain from each variety. To harvest each individual plot, the combine cuts and takes up the mature plant material. Like large-scale combines, the cut plant is then threshed within the machine, the straw is sent out the back, and the grain is funneled to a chute where it is bagged for collection. Once all of the grain has moved through the combine and funneled down the chute into the bag, a researcher removes the bag, ties it closed, and attaches the corresponding harvest tag for identification. They then wrap a new harvest bag around the chute in preparation to catch the grain from the next plot to be harvested. This process is repeated for each research plot in a study until all of the grain has been collected.