So now where do you go in Marin County to get a good pastrami sandwich?

The San Rafael location of Miller’s East Coast Delicatessen unceremoniously shut its doors last week after operating in the Montecito shopping center on Third Street since January 2012.

The Jewish-style deli’s longtime San Francisco location on Polk Street will remain open.

Since the closure of the San Rafael shop, owner Robby Morgenstein also has stopped supplying the café at the Marin JCC with grab-and-go items such as sandwiches, baked goods and matzah ball soup.

“It’s been a tough four years, I’ll tell ya,” Morgenstein said, summing up a San Rafael run plagued by rising wholesale food costs, sparse breakfast and dinner crowds and “multiple issues” with his managers and chefs. “I had a hard time finding good people to run it,” he said.

The 3,000-square-foot restau­­­­­rant, which had 126 seats including the patio, closed on June 17. The somewhat tucked-away corner spot is up for lease, although Morgenstein is on the hook through January 2016 if no new tenant emerges.

“It was very busy for lunch, but just for lunch,” Morgenstein explained. “Dinners never took off, and breakfasts were pretty quiet. Couple that with the inflation of food costs over the last few years, and this location never really made a profit. I put all my money into it. I just don’t have any more to put in.”

Morgenstein said the San Francisco Miller’s, which has only 49 seats and, at 1,640 square feet, is half the size of the San Rafael location, takes in $7,000 to $10,000 more per week.

“It was a stressful four years. Now it’s time to get myself back in shape, and dedicate myself to the San Francisco store for awhile,” he said. “I do have some ideas for other stores, but mostly small, takeout-based places. I’m not sure I want to jump into another 3,000- or 4,000-square-foot, 100-seat restaurant.”

A Baltimore native in his early 50s, Morgenstein moved west when he was in his 20s and worked as a chef. He opened Miller’s East Coast West Delicatessen at 1725 Polk St. in August 2001, then closed it three years later to refurbish the location and rethink his strategy. When he opened again several months later, he dropped the “West” from the deli’s name.

Morgenstein started working on a second location in 2011, opening on Jan. 4, 2012 in San Rafael, not too far from his home in Novato. Now, he will have a longer commute, as almost all of his time will be spent in San Francisco.

“I dragged out the closing of the Marin location longer than it should have been,” he said. “I should have done it in the fall of 2014. I had repriced the menu again, one more time, but then began realizing that raising the prices wasn’t going to even cover my costs. And I didn’t want to be the guy selling a pastrami sandwich for $19. This is not New York, where people are used to getting a huge, overstuffed sandwich but paying $24 for it.

“When I realized I’d have to raise prices a second time, that’s when I decided to shut it down.”

Morgenstein said a case of eggs used to be $21, but now he’s paying $51, and the pastrami he bought for $3.89 a pound is now $7.55. “The price of center-of-the-plate proteins has pretty much doubled in the last four years,” he said. “Chicken and beef have gone through the roof.”

To that end, he has slightly altered the offerings at the San Francisco location. The smoked fish selection has taken the biggest hit, with no more sturgeon, sable, kippered salmon or herring on the menu, although whitefish and nova salmon remain.

The restaurant is also featuring “Cincinnati Chili,” “Sicilian Pizza” and other nontraditional items alongside its long lineup of Jewish deli classics.

Morgenstein said he’s had a “ton of emails” from people saying, “Wish you were still here” and “So sorry it didn’t work out.” He said many also have told him the restaurant “was the best thing we had in Marin.”

The restaurant will continue doing catering jobs in Marin, and a sliver of its presence will remain at the Osher Marin JCC in the form of weekly senior Shabbat lunches, which Miller’s caters. And which Morgenstein often attends.

“That is the best part of my week, bar none,” he said.