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Plant-based food and cereals is sometimes very emotionally discussed by dog owners. Particularly critical are aspects of animal welfare as well as increasingly those of CO2 footprint. The suitability of cereals is also questioned, with an increasing demand for "pseudo-cereals," which do not contain gluten. In this study, 10 Beagle dogs were fed in a cross-over design with diets that contained poultry or legume protein as a mix of peas and bean concentrate with or without the addition of a cereal (processed wheat flakes) or the “pseudo-cereal” quinoa. The experimental setup was a three-factorial design where the first factor represents the carbohydrate, the second the protein component and the third the dietary protein concentration. Protein levels were adjusted to fulfil the needs of dogs for essential amino acids or to 1.5 times the amount of protein and amino acids compared to the maintenance requirement. After a three-week adaptation phase, the collection of faeces, urine and blood samples took place in the fourth week. Statistical evaluation included three-factorial ANOVA and Tukey tests (p < 0.05). The type of protein in the diet variants influenced (p < 0.001) the richness of microbial sequences detected in the faeces. The highest values for richness of the faecal microbiota were observed with diets based on animal proteins. Diets based on animal proteins increased the faecal occurrence of Fusobacteria (p < 0.001), while dietary variations with plant proteins favoured the relative occurrence of Actinobacteria (p = 0.040). The pH values in the urine of dogs on diets containing wheat and poultry protein (5.73–6.30) were lower compared to diets with quinoa (7.20–7.47). An exception was the combination of wheat with the plant protein source, where a higher pH value was observed (7.42) when administering the higher protein dosage. As expected, urinary nitrogen concentrations increased with higher protein intake. The protein sources led to minor changes in haematological parameters, while serum urea and albumin concentration was significantly influenced by the protein content in the experimental feed (p < 0.001; p = 0.004). With the use of quinoa, the activity of alanine aminotransferase increased compared to wheat-containing diets (p = 0.017), and higher bilirubin concentrations were also observed (p = 0.031). The activity of alkaline phosphatase increased with quinoa compared to wheat-containing diets (p = 0.030) and was lower with a higher protein content in the feed than with an adequate supply (p < 0.001).