Ronan De Leon went into a brief panic last month when the delivery man failed to show up with the eggs that the Parkside café and bakery depends on. His anxiety spiked yet again when he arrived at the Smart & Final grocery warehouse in San Rafael, hoping to cover the missing order.

“I was shocked to find out that there were no eggs,” recalled Mr. De Leon, who has worked at the Stinson Beach establishment for 15 years and now manages it. “I went to the store and saw that everything was empty. I kind of freaked out, because it was Friday, and it was going to be a busy weekend.” 

For several weeks now, the highly pathogenic strain of bird flu striking poultry flocks across the nation has led to empty shelves around the Bay Area and the state. 

In West Marin, restaurant and bakery managers have scrambled for alternative supplies when their regular sources have come up empty. Meanwhile, customers are shelling out $9 for a dozen eggs—close to the same price they would pay to small producers of bespoke eggs, some of whom are benefitting from the market shift. 

Many stores, including the Palace Market and Good Earth, have posted signs restricting sales to one or two cartons per customer, beseeching people to refrain from panic buying. Even large outlets such as Costco have occasionally found their shelves empty in recent months.

Both Mr. De Leon and Darcy Matteucci, the co-owner of Brickmaiden Breads in Point Reyes Station, sourced eggs from Clover Sonoma until about a month ago, when they stopped coming. 

After failing to find any eggs at the Smart & Final, Mr. De Leon ordered several cases from Sysco, a nationwide grocery supply chain. Ms. Matteucci turned to her produce supplier, who managed to locate the roughly 45 dozen eggs she needs each week to produce the pastries, pies and quiches that are her stock in trade, along with bread. (Fortunately, her sourdough loaves only require a magical blend of water, flour and salt.)

“I’ve been having to jump through hoops trying to figure out where I can get eggs,” Ms. Matteucci said. “I’m getting whatever I get.”

She prefers to purchase local, organic eggs but will use non-organic in a pinch. So far, she has avoided raising prices, but she’s not sure how much longer she can keep producing quiche without charging more. 

Each quiche requires 13 eggs and yields nine pieces. At $9 a slice, the servings are already so expensive that Ms. Matteucci cringes a bit when disclosing their price. 

“It’s the quiche that’s tripping us up,” she said. “We can either make the choice of taking it off the menu or telling our customers we have to raise the price. We know you love the quiche, but eggs are expensive.”

Major bird flu outbreaks in Sonoma County last year required the slaughter of more than 1 million chickens and ducks, and two smaller outbreaks in Marin required the culling of some 150,000 birds, according to the California Department of Food and Agriculture. Statewide, more than 10 million birds were culled over the last year. Most of the biggest outbreaks have taken place at industrial-scale operations in the Central Valley.

So far, West Marin’s smaller commercial flocks have remained unscathed. In fact, for small-scale producers like Anna Erickson of Hands Full Farm in Tomales, there have been benefits to the shortage, although she worries about her birds every day.

Ms. Erickson sells her pasture-raised eggs at farmers markets around the region for $11 or $12 a dozen—a price too high for many customers in ordinary times. But she’s been selling out since the shortage hit, as the rising price of ordinary eggs approaches that of her specialty varieties.

“We’ve been lucky so far,” Ms. Erickson said. “I still have my chickens. And it’s easy for me to sell my eggs at the farmers market, because people just are so desperate to get good eggs.”

Nor has she used the shortage as an excuse to jack up her prices. With feed and labor costs remaining steady, she sees no need to gouge anyone. “Why should I change the price of my eggs just because people are desperate?” she said.

The C.D.F.A. has warned her a couple times that her farm was near Sonoma County outbreaks, but not so close that she had to take any drastic measures. Still, she worries that her flock of about 1,000 hens could be struck at any time.

“Every morning, I wake in a panic that I’m going to look out my windows, and all my chickens are dead on the ground,” she said. “I’ve been doing that for about, you know, a year and a half now.”

Marin is fortunate that its poultry producers are small operations, unlike their massive counterparts in Stanislaus, San Joaquin or Merced Counties, said Joe Deviney, Marin’s commissioner of Agriculture, Weights and Measures.

“The bird flu is just one more example of why we need a multitude of small family farms,” he said. “They’re more resilient. If you have a million birds in a huge farm, one little mess-up somewhere in the whole chain, it has a huge impact. The small family farms are so important to keep food production sustainable. And the more they go away, the more we’re reliant on these huge farms.”