Bacteria of the genus Enterococcus are an integral part of the gastrointestinal (GI) tract of the animal microbiome and can be found in fermented meat and dairy products, mostly due to poor food handling and their ability to grow under extreme conditions. Bacterial infections are treated with antibiotics, and the rise of enterococci, which are resistant to a variety of antibiotics and have the ability to transfer genetic material, is a notable problem in modern medicine. The uptake of heavy metals in animal feed and resistance to them has been associated with resistance to glycopeptides and macrolides for many years. We wanted to determine the presence of genes encoding for acquired resistance to antibiotics and heavy metals like copper. To this end, enterococcal isolates from different ecosystems were used in this study. The enterococcal isolates were obtained from the faeces of wild boar (Sus scofa) (n = 30), spontaneously fermented sausages produced from the meat of wild boar and domestic pigs (Sus domesticus) (n = 10), and traditionally produced Istrian cheese (n = 5). Antibiotic-resistant genes for erythromycin and tetracycline and those for heavy metal copper were confirmed using multiplex PCR methods. The gene coding for erythromycin was found in 33.33% of faecal isolates, in 20% of cheese isolates, and in 10% of sausage isolates, and the gene coding for tetracycline was found in 80% of faecal isolates, in 20% of sausage isolates, and in none of the cheese isolates. A gene coding for copper was detected in 56.66% of the faecal isolates, then in 40% of the cheese isolates, and 30% of the sausage isolates. Our results suggest that genes encoding for acquired resistance to antibiotics and the heavy metal copper are present in the collected enterococcal isolates, and that even though isolates were collected from different ecosystems, they show similar trends for the presence of resistance genes.