Canine atopic dermatitis (CAD) is a common chronic allergic skin disease. In our previous study, we isolated two probiotic strains, Lactococcus cremoris subsp. cremoris MP01 and Lacticaseibacillus paracasei subsp. paracasei MP02, from Mongolian fermented milk. These strains demonstrated potential in alleviating symptoms similar to AD and reducing specific immunoglobulin E (IgE) levels in a mouse model of AD. Building upon this discovery, our current investigation sought to evaluate the therapeutic potential of these probiotics for treating CAD. We conducted an open-label, single-arm clinical trial where dogs diagnosed with AD were administered LCP capsules containing Lc. cremoris subsp. cremoris MP01 and L. paracasei subsp. paracasei MP02 once daily for 60 days. Stool, skin swab, and venous blood specimens were collected at three intervals: before, and after 30 and 60 days of LCP intervention. The skin and fecal microbiomes were analyzed using full-length 16S rRNA sequencing. After 60 days of LCP intervention, notable improvements were observed in skin lesions and scratching behaviors, accompanied by reductions in both the Canine Atopic Dermatitis Extent and Severity Index (CADESI) and the Pruritus Visual Analogue Scale (PVAS) scores. Additionally, LCP intervention resulted in significant reductions in IgE levels and modulation in type 1 T helper (Th1)/ type 2 T helper cells (Th2)-related cytokine secretion. Microbiota analysis unveiled changes in the composition of both skin and gut microbiotas, including reductions in Shigella flexneri on the skin and Romboutsia in the gut. Levels of short-chain fatty acid (SCFA) increased following the 60-days of LCP intervention. These effects were likely mediated by alterations in gut microbiota and the upregulation of SCFA levels, which subsequently reduced the secretion of allergy-related IgE. Collectively, these mechanisms contributed to alleviating CAD symptoms, regulating skin microbiota composition, and reducing the adherence and invasion of environmental microbes and pathogens. Overall, our findings highlight the promising therapeutic potential of the Lc. cremoris subsp. cremoris MP01 and L. paracasei subsp. paracasei MP02 mixture as an effective strategy for managing CAD in dogs.