Urban agriculture advocates survived a scare and scored an important victory Tuesday, when the San Jose City Council backed off a proposed $1,540 fee that could have left green-thumb dreams dying on the vine.

Last month, community groups were elated to learn the council would grant owners of blighted vacant lots a significant property tax break for converting parcels into small-scale farms for five years. But then the city decided to charge owners a $1,540 fee to apply for the tax break.

Jamie Chen, an organizing manager of Sacred Heart Community Service’s La Mesa Verde program, which promotes organic gardening in low-income areas, has worked for two years to push through the policy. She said she was “flabbergasted at how they came to such a high fee.” On Tuesday, Chen and more than a dozen other speakers begged the council to reduce or drop the fee altogether. They pointed to San Francisco and Sacramento as places that don’t charge any fees.

“It was a big surprise,” Chen said of the council’s decision to drop the fee. “We didn’t think that they would change.”

Council members were taken aback when speakers accused them of caring more about the city’s minimal costs than helping communities struggling to grow fresh food. Mayor Sam Liccardo and downtown Councilman Raul Peralez, who had worked with Chen on the Urban Agriculture Incentive Zone measure, initially were poised to support the $1,540 fee but quickly changed course. Rather than charge applicants for 10 hours of staff work, the council decided to lower the fee to $308 for two hours of staff time. The city will monitor how much staff time is actually required and, if necessary, bill the applicants for any additional time.

Peralez and Vice Mayor Rose Herrera then went a step further and agreed to pay the initial fees for the first set of applicants out of their own office’s discretionary funds. Peralez has far more eligible vacant lots in his downtown district than other council members.

Under the new program, property owners of an acre or smaller must turn their vacant lots over for five years of farming. In return, their parcel will be assessed at a reduced rate of $12,700.

Raul Lozano, executive director of Valley Verde, a nonprofit that helps ethnic communities learn to grow their favorite organic crops, said the council’s decision to lower the application fee is a huge victory. The organization intends to build a greenhouse for seedlings. The group’s West San Carlos Street site will also be used for raised beds and equipment storage.

Property owner Thang Do, who owns a supermarket in San Jose’s SoFA district, said the higher fee wouldn’t have been a “deal breaker” because he’s a committed urbanist, but he was happy to be the one to kick off a worthwhile program.

“I think it’s the right thing for the city to do, to reduce the fee, because there are so few of us that are willing to do this that the cost to the city wouldn’t be that great anyway.”