To deliver their colorfully decorated packages, monthly subscription services must defy some of the fundamental rules of e-commerce.

The multibillion-dollar industry is powered by complex packing and shipping, often performed manually from sprawling warehouses. They must receive and store batches of entirely new products each month. When it’s time to ship, the products are lined up along conveyor belts so workers can arrange them in the exact same formation tens—or hundreds—of thousands of times during a frenzied week of packing.

For beauty boxes, the products are often wrapped with tissue, ribbon, stickers and other flourishes to protect delicate objects and give subscribers a sense of luxury. They’re usually shipped out in three waves so customers in one region of the country don’t receive their boxes before customers elsewhere. And because the product mix changes, the whole process starts from scratch each month.

The most successful online retailers, by contrast, are the ones that make the most efficient use of warehouse space and automate as much of the shipping process as they can. The subscription services are a more manual business, and each company has distinct logistical complications.

A finished Birchbox package for men, left, and women packed at the production facility in Mount Juliet, Tenn. The monthly subscription service sends customized samples of beauty products to its subscribers. Photo: Joe Buglewicz for The Wall Street Journal

Beauty boxes from Glossybox arrive filled with “sizzle,” the industry term for strips of crinkled tissue paper that holds contents in place. Items are wrapped together in a sheet of tissue paper, sealed with a sticker, and tied with a ribbon inside the boxes. “Doing the bow 500,000 times is not easy. Some people just cannot do this,” said Britta Fleck, president of Glossybox U.S.A. “It sounds ridiculous, but if the box is open and it’s not a nice bow, the experience is already lower.”

Glossybox packs its products in sturdy gift boxes that don’t fold or stack, which are then placed inside another cardboard box to be shipped. The boxes take up so much space that it is costly to transport the packaging from its supplier in China to its warehouses around the world, Ms. Fleck said. Ms. Fleck and her team sent almost 200 test boxes to themselves when the company first started to find packaging that looked attractive but was still strong and small enough to ship profitably. The Berlin-based company ships 275,000 boxes each month.

Rival Birchbox ships 100 different combinations of products, or kits, and a total of over a million boxes globally each month. The order in which products are arranged for assembly is important, said Pooja Agarwal, vice president of operations. Workers must be able to finish packing one kit and start on the next, with a minimum amount of rearrangement, and in as little time as possible.

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Though Birchbox has reached a scale at which it can at least automate the placement of address labels, much of what it does is still manual, Ms. Agarwal said. Warehouse workers have to be trained to do multiple jobs such as receiving and stocking products as well as packing and shipping them so they’re not idle in the weeks between shipments. And at peak shipping times, the company sometimes borrows workers from other shippers, and hires temporary workers. Birchbox uses Geodis SA’s logistics provider OHL which operates the warehouses.

New Beauty’s TestTube, a bimonthly subscription, makes instructional videos for warehouse managers showing the optimum placement of every product because they ship in a cylindrical package that can be a tight fit.

“We looked at robot arms but they’re shipping different things every month. Clients change their boxes all the time. So it would be too costly,” said Bob Formica, chief operating officer at Fosdick Fulfillment Corp., a logistics company in Wallingford, Conn., which ships about 800,000 subscription boxes a month including boxes for TestTube.

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Surprise-in-a-box subscriptions could be a fad, of course. If sales cool and venture funding dries up, subscription businesses with high logistics costs will be put to the test. Birchbox, which is one of the oldest and largest subscription services, cut 15% of its staff earlier this year. Its revenue rose by 24% last year, estimates Slice Intelligence, a Palo Alto., Calif., firm which conducts market research based on an analysis of emailed consumer receipts. Birchbox has been experimenting with other business models, including its own makeup brand and brick-and-mortar shops.

Meanwhile, customers follow the progress of their packages closely. Rants about late-arriving packages and photos and videos of broken mirrors or spilled nail-polish spread quickly on websites devoted to subscription boxes.

“Something people are weirdly obsessed over is shipping weight,” said Laura DiNicola, who spends about $1,000 a year on subscriptions. Fans will begin to speculate on online forums that the box is lighter than usual. The first people to get their box often post “spoilers,” as if they are getting sneak peeks to a highly anticipated TV show.

Petit Vour, a Dallas-based beauty box which promises that its items are all natural and aren’t tested on animals, decided to pack all 7,000 of its monthly subscription boxes in its own offices after a contractor mistakenly swapped the address labels for 500 of its subscribers with the subscription list for another beauty box company.

“It was particularly bad because our subscribers are looking for cruelty-free vegan products. They’re ingredient sleuths. So to receive a box of goods that are not that at all, they were very confused,” said Madeline Alcott, the company’s co-founder.

Write to Loretta Chao at loretta.chao@wsj.com