Agriculture expansion and intensification are having a huge impact on plant and arthropod diversity and abundance, affecting food availability for farmland birds. Difficult food access, in turn, can lead to immunosuppression and a higher incidence of parasites. In studies designed to examine changes in the diet of birds and their parasites, metabarcoding is proving particularly useful. This technique requires mini-barcodes capable of amplifying the DNA of target organisms from faecal eDNA. To help understand the impact of agricultural expansion, this study sought to design and identify mini-barcodes that might simultaneously assess diet and intestinal parasites from the faeces of farmland birds. The capacity to identify diet and parasites of two existing and three developed mini-barcodes was tested “in silico” in relation to the behaviour of a reference eukaryotic primer set. Of the mini-barcodes tested, MiniB18S_81, one of our designs, showed the higher taxonomic coverage of eukaryotic taxa and a greater amplification and identification capacity for diet and parasite taxa sequences. This primer pair was tested on faeces samples from five different steppe bird species. According to our data, this barcode shows good taxonomic resolution of the most relevant diet and parasite phyla, Arthropoda, Nematoda, Platyhelminthes and Apicomplexa, at the order level. The mini-barcode developed emerges as an excellent tool to simultaneously provide detailed information regarding the diet and parasitology of birds, essential for conservation and management.