A small group of beekeepers in Mexico has inflicted a blow on biotech giant Monsanto, which has halted the company’s ambitions to plant thousands of hectares of soybeans genetically modified to resist the company’s pesticide Roundup.

A district judge in the state of Yucatán last month overturned a permit issued to Monsanto by Mexico’s agriculture ministry, Sagarpa, and environmental protection agency, Semarnat, in June 2012 that allowed commercial planting of Roundup-ready soybeans.

The permit authorised Monsanto to plant its seeds in seven states, over more than 253,000 hectares (625,000 acres), despite protests from thousands of Mayan farmers and beekeepers, Greenpeace, the Mexican National Commission for the Knowledge and Use of Biodiversity, the National Commission of Natural Protected Areas and the National Institute of Ecology.

In withdrawing the permit, the judge was convinced by the scientific evidence presented about the threats posed by GM soy crops to honey production in the Yucatán peninsula, which includes Campeche, Quintana Roo and Yucatán states. Co-existence between honey production and GM soybeans is not possible, the judge ruled.

Mexico is the world’s six biggest producer and third largest exporter of honey. About 25,000 families on the Yucatán peninsula depend on honey production. This tropical region produces about 40% of the country’s honey, almost all of which is exported to the EU. This is not small change: in 2011, the EU imported $54m (£32m) worth of Mexican honey.

The concerns are multiple. Roundup-ready crops – soybeans, corn, canola, sugar beets, cotton and alfalfa – have been manipulated to be resistant to glyphosate, the active ingredient in Roundup.

Some argue that glyphosate poses a risk to human and animal health, a claim that Monsanto and other agribusinesses reject.

In addition to health risks, environmental damage to soil, water and bee colonies – which are dwindling fast – have been attributed glyphosate use, threatening food and water security across the globe.

GM crops could devastate the important European export market for Mexican beekeepers, where the sale of honey containing pollen derived from GM crops has been restricted since a landmark decision in 2011 by the European court of justice.

The ruling barred honey derived from a GM crop unapproved for human consumption – which includes some soy and other animal feeds – from sale in the EU. Honey with more than 0.9% of GM pollen (from an approved GM food) must be labelled as containing GM ingredients and cannot be marketed as an organic product. Some countries, including Germany, reject honey that contains any GM pollen.

A small study conducted in Campeche, where about 10,000 hectares of GM soybeans were planted after the permit was approved in 2012, found GM pollen in some honey samples destined for the European market. This, say the authors, threatens the local honey industry and contradicts the position taken by Sagarpa and industry groups that soybeans are not visited or pollinated by bees searching for food because they can self-pollinate.

The Monsanto ruling was commended by the respected national newspaper La Jornada, which accused the Mexican government of ignoring widespread concerns over GM and forcing those opponents to fight it out in court with powerful multinational companies. The government’s stated ambition of eliminating hunger is incompatible with its decisions to increasingly allow multinational companies such as Monsanto to introduce GM crops, the paper’s editorial concluded.

Central to the ruling was the Mexican constitution, specifically the government’s obligation to fully consult indigenous communities before making any major decision about what happens, including what is grown, on their territory. The judge ordered planting to stop and gave Sagarpa six months to carry out full and proper consultations with indigenous farmers – which it should have done before the permit was granted in 2012.

It was this same omission that led to an almost identical ruling by a district judge in Campeche in March 2014.

These two judgments have set a precedent that will help farmers, campaigners and environmentalists take local legal action against the rollout of GM soy and corn, which the federal government is sanctioning without consultation and against experts’ advice.

But this is a high-stakes game to play, in which indigenous communities are being forced to fight their own government and multinational corporations with multimillion-dollar legal departments, simply to have their constitutional rights honoured and protect their traditional ways of farming and living.

So while a third victory in Chiapas, where a similar case is pending, could soon follow, this is almost certainly only round one. Monsanto will probably appeal against the decision to a higher court.

The North American Free Trade Agreement, criticised by some for crippling small-scale Mexican farming, is not on the side of the beekeepers. This David and Goliath battle is about so much more than honey.