Brazil is among the world’s largest consumers of pesticides, with glyphosate (GLY) being the most commercialized herbicide in the country. Studies showed microorganisms suffer selective pressure when exposed to pesticides, developing tolerance to pesticides and resistance to antibiotics (ABs), in a phenomenon known as “cross-resistance”. The present work aimed to evaluate the occurrence of glyphosate-tolerance and AB-resistance in bacteria isolated from different agricultural management systems in Ceará State, Brazil. Gram-negative bacteria isolated from agroforestry (S1), conventional farming (S2) and uncultivated (S3) soils were cultured in the presence of 1.6% acid glyphosate. Overall, 58 strains were isolated. Soils S1 and S2 presented several multidrug resistant (MDR) strains, the majority resistant to ampicilin. Although there was a small percentage of strains resistant to ertapenem (33%, soil S1), the fact they were found is concerning, as Carbapenem antibiotics are used to treat clinical cases of MDR bacteria, which are not common outside hospital settings. Stenotrophomonas maltophilia (soil S2), resistant to six of the eight ABs tested, was identified by MALDI-TOF mass spectrometry, and was found as one of the most common opportunistic bacteria in ICUs of Ceará hospitals.