Unlike most artisan cheese makers, Beecher's mainly uses pasteurized milk and operates a high-volume modern production facility, with multiple farms supplying milk. When Beecher's encountered problems in guaranteeing the standard flavor of the milks they were using to make cheese, the company bought their own herds of dairy cattle and farms to ensure control of the cheese products from beginning to end. Beecher's uses various cheese cultures when mixing cheeses, so a cheddar cheese produced by Beecher's may use cultures not normally intended for cheddar cheese production.
Beecher's Pike Place Market location includes a retail shop, and sells both Beecher's cheeses and others brands from local Pacific Northwest cheesemakers. Beecher's also manufactures and sells macaroni and cheese dishes, which have received praise in reviews from the national news media. Dammeier and his firm's cheeses have been featured on national television, including The Martha Stewart Show. A cookbook by Dammeier, Pure Flavor: 125 Fresh All-American Recipes From The Pacific Northwest, has been published, and incorporates recipes used to make various Beecher's products and dishes. In addition to their various business endeavors, Beecher's sponsors Pure Food Kids, an educational program to teach children in the Seattle public schools system about healthy diets.
After taking a cheese making course at Washington State University, Dammeier decided he needed to hire someone to work with him as chief cheesemaker. He hired Brad Sinko, a microbiologist, who previously had managed his family cheese business of Bandon Cheese in Oregon, before it was acquired by the Tillamook County Creamery Association. According to Dammeier, the artisanal cheese market was underrepresented in Seattle and Washington, and he opened his business in part to encourage more cheese business to grow in the region. In 2000, Washington had nine licensed cheesemakers; this expanded to twenty-eight by 2007. Dammeier compared the growth he expects in artisan cheese to the United States' recent growth in sales of specialty beers:
"If you said the word 'Porter' 20 years ago, no one in the U.S. would have had any idea you were talking about beer. Twenty years from now, people will know what a washed rind is."
Thanks to financing from Dammeier's other business ventures, Beecher's had the ability to build up their operations slowly, absorbing the costs of capitalization of the business while experimenting with their cheeses, including the time to age them. "The first vat," remarked Dammeier, "we threw away. The second vat was really good." As their work progressed Sinko would adjust the formulas of their cheese processing, the cultures, and the enzymes involved, and increased the average aging time for their Flagship brand to 18 months. However, they only publicly claim 12 months of aging. In their first year of operation, Beecher's had no aged product of their own to sell, instead building up an inventory of of cheese. During that same time, their primary sales were of fresh cheese curds.
To ensure a standardized flavor for the finished cheeses, and due to there being insufficient space in their facilities for milk separating systems, Sinko said he "went and standardized the herd." Their initial milk from Holstein cows was sweet, but lacked the fatty content and nuttiness of Jersey cow milk that was part of the product they wanted to create. They were able to eventually balance the two to their satisfaction. Dammeier has described the blend of Holstein and Jersey milk as a "50–50 mix". From each farm, all the milk supplied to Beecher's is from the same herd, to ensure that the flavor of each batch of milk they receive is consistent (based on the herd's diet and environment).
At times, Beecher's has encountered challenges in maintaining this uniform standard. For example, when flooding affected one farm, the cows there produced enzymes in their milk that helped their calves to fight off bacteria, but changed the flavor of the milk.
The cheese factory is housed in a small, glass-walled facility in Seattle's Pike Place Market, on Pike Place between Stewart Street and Pine Street. The location includes a retail shop and a café that features cheese-based meals. Passers-by in the heavily touristed market can watch the cheese making process. Beecher's produces over pounds of cheese annually. Their manufacturing facility now operates twenty-four hours a day to keep up with their demand.
Sinko admits that the modern facility with large vats of cheese and milk processing would seem to contradict the word "Handmade" in the company name. According to him, all of the cheese is monitored, processed, and prepared by hand, but simply on a larger scale than most artisanal cheesemakers. Unlike most artisan cheeses, Beecher's is made largely with pasteurized milk. Dammeier believes that many people feel raw milk cheeses taste better due to renowned French cheeses, which were historically made of raw milk because the farms were unable to afford pasteurization. "I've probably tasted 150 different cheeses this year, and I'm convinced that raw milk doesn't create more flavor," he said, adding that his cheeses have a more consistent taste from not using raw milk. Nevertheless, Beecher's offers a raw milk version of their Flagship cheese. The cheeses they produce use no artificial ingredients or preservatives. Beecher's typically manufactures up to nine different varieties of cheeses each year, including a combination of their staple brands and various seasonal varieties.
At the Beecher's facility, their process for cheese manufacturing is multi-staged. Thousands of gallons of milk are hose-fed from delivery trucks into the manufacturing area, where it is heated to complete the pasteurization of the milk. The heated milk is processed into a stainless steel trough, and the temperature further increased, while the first live cheese cultures and rennet, a coagulant, are added to the developing mixture. According to Amir Rosenblatt, a cheesemaker at Beecher's, the heating and cheese temperatures used in their cooking process are tightly controlled. "A variation of half a degree [in the pasteurization process] can change the flavor of the cheese," he said. Cheesemakers use stainless steel "rakes" to then gather the milk mixture, before allowing it to settle briefly, at which point the cheese is cut repeatedly by hand until it achieves a yogurt-like texture and substance. This process is repeated often, until a desired consistency is reached. The mixture is then drawn away to a new trough where most of the remaining water and whey is drained from the cheese. While the whey is continually pulled from the cheese, cheesemakers constantly separate the cheese by hand into smaller and small stacks of cheese curds, which form as the whey is removed. To complete the curding, a large amount of salt is added to cure the cheese and draw still more whey from it. The curds are finally cut into portions, filled into cheese molds, stacked on top of each other, and the remaining excess moisture is forced from the cheese with a constant of pressure for at least 24 hours, before the finished cheese is stored to age. For every of milk and whey, Beecher's will typically create of finished cheese.
Beecher's cheeses differ from similar cheeses in that they mix cheese growth cultures in unusual ways. For example, their signature "Flagship" cheese includes cultures typically used for non-cheddar cheeses, such as Gruyère and Emmental, changing the nature, flavor, and texture of their cheddar. Flagship cheese is produced using a cheddaring process, but owing to a different taste, Beecher's does not call this cheese cheddar. The cheese has been described as having a "sweet finish and creamy texture" unlike the tangier cheddars, owing to this being one of the cheeses they create with a mixture of different cheese cultures. After being prepared in blocks and aged for approximately one year, the Flagship—unlike cheddars—lacks a rind, is moister, resembles butter visually, and carries a milky aroma due to being aged in plastic bags. A variant called "Flagship Reserve" is aged in cheese cloth in sizes on racks in open air, and is rubbed with butter while being turned daily. This preparation method causes the Reserve to lose up to 12% of its initial weight by the time it is completed. The Reserve is aged for a shorter amount of time, leading to a sharper, nuttier taste and texture, according to Food & Wine Magazine. Of the of cheese they produce annually, approximately will be Flagship, and only will be Flagship Reserve.
As of 2006, a second cheese making center was opened in South Seattle. This second location includes a cheese aging facility. Additionally, Beecher's is in the process of developing new types of crackers, designed to not overpower the taste of the cheese with which they are paired.
Beecher's features a gourmet cheese shop and café in their Pike Place Market facility. It is considered an anchor of the Pike Place Market, and has become a tourist attraction in its own right. During the day, crowds typically gather in the store, watching through windows as the cheesemakers prepare batches of cheese.
A portion of the cheese curds used in the manufacturing process is set aside to sell directly to visitors at the retail store. The principal cheeses created and sold by Beecher's are their Flagship and Flagship Reserve varieties; "Just Jack", a form of Monterey Jack cheese; "Blank Slate", a type of cream cheese; unpasteurized, raw-milk versions of their Flagship cheeses, and various cheeses seasoned and flavored with spices and herbs. Some of their seasonal varieties have included cheeses similar to Brie.
The Pike Place Market store now sells roughly thirty-five other local artisan cheese brands, in addition to the various Beecher's products. The Pike Place Market location also offers classes to the public about cheese making, cheese history, and the pairing of wine with cheese. The collection of Pacific Northwest cheeses on sale at the retail store has been described as the best in the entire region by Will O'Donnell in Northwest Magazine. In keeping with Dammeier's idea that his cheese business should encourage the growth of the artisan cheese businesses in the area, the Beecher's retail store makes special efforts to feature and sell cheeses from new and small Northwest cheesemakers.
Beecher's are sold in retail stores beyond the Seattle area, including locations in San Francisco and in New York City at well-known artisanal cheese vendors such as the shops of Murray Klein and the international Artisanal Cheese retail company.
Fourth through sixth grade elementary school children are educated on the effects of food additives, eating healthy foods, reading food labels, and about marketing of food aimed at children. According to Chip Wood, co-founder of the Northeast Foundation for Children, fourth through sixth grade children will typically be between the ages of 9 and 12 years old. The program is provided to no cost to the children and their families. To date, 3,500 children have participated in the educational program. Pure Food Kids is taught in classrooms, after-school events, and at Parent-Teacher Association events, with all supplies and materials provided by Beecher's, although there is explicitly no promotion or use of any products from any of Dammeier's businesses.