Probiotics in almond-based matrices were considered as a means of obtaining fermented products which would cover both the current demand for health-promoting foods and for alternatives to standard yoghurts. Firstly, the combined effect of high pressure homogenisation (HPH) and heat treatment on the physical stability of almond “milk” was studied. The beverage was homogenised by applying 62, 103 and 172 MPa (MF1, MF2 and MF3 respectively); MF3 was also combined with two different heat treatments (85 °C-30 min (LH) and 121 °C-15 min (HH)). Both microstructure and colloidal stability were analysed in all the processed samples to select the most suitable treatment with which to obtain a stable product. The selected almond milk was then fermented with probiotic Lactobacillus reuteri and Streptococcus thermophilus and the final product was characterised throughout cold storage time (28 days) as to pH, acidity, serum retention and starter viability. A sensory evaluation and probiotic survival to in vitro digestion was also conducted. The results showed that the physical and structural almond-milk properties were affected by both HPH and heat treatments, obtaining the greatest stability in MF3-LH samples. The fermented milk permitted probiotic survivals above the level suggested as minimum for ensuring health benefits during the entire controlled time and, hence, can be considered as a functional food. No differences in the sensory acceptability of the product were found between 1 and 28 storage days. Therefore, a new, functional, fermented product was developed, which was suitable for targeted groups, such as the lactose-intolerant and cow-milk-protein allergic populations.