Malolactic fermentation (MLF) is a biological process of deacidification of wines that may also help to increase the microbiological stability of the product and to enhance its sensorial attributes, in particular its aromatic profile. MLF can occur spontaneously due to the presence of indigenous bacteria in the environment of fermented beverages such as wines and ciders. However, the inoculation of lactic acid bacteria (LAB) starter cultures could prevent potential losses and standardize the process. The industrial-scale production of these starter cultures requires cost-effective, sustainable, and feasible approaches. A possible approach to acquire bacterial biomass, while addressing waste disposal concerns, is the use of by-products from the apple juice industry, such as apple pomace. Moreover, to ensure the long-term viability and activity of starter cultures, appropriate preservation methodologies need to be developed. Thus, the aim of the present study was to evaluate the growth of two Lactiplantibacillus plantarum strains, UNQLp11 and UNQLp155, in supplemented apple pomace and to optimize the preservation conditions. Cultures were either frozen or freeze dried (trehalose (20% m/v) as a protective agent, potassium phosphate buffer (pH 7), and a combination of trehalose and buffer), and then cell viability and malolactic activity were analyzed under wine stress conditions. Notably, the combination of phosphate buffer at pH 7.0 and trehalose emerged as the most effective preservation strategy for freeze drying, exhibiting enhanced viability and malic acid consumption for the two strains evaluated. These findings underscore the inexpensive and sustainable viability of using a semi-solid medium formulated with apple pomace for LAB biomass production and subsequent preservation.