Red, yellow, and green peppers are vegetables rich in natural pigments. However, they belong to seasonal vegetables and need to be treated to prolong their shelf life. One new approach to processing vegetables is to pickle them using lactic acid bacteria. The use of such a process creates a new product with high health value, thanks to the active ingredients and lactic acid bacteria. Therefore, this study aimed to evaluate the effect of the applied strain of lactic acid bacteria (LAB) on the chemical properties, including the content of active compounds (pigments) and the physical properties of the peppers. Levilactobacillus brevis, Limosilactobacillus fermentum, and Lactoplantibacillus plantarum were used for fermentation and spontaneous fermentation. The pigments, polyphenols content, and antioxidant properties were determined in the pickled peppers, as well as sugar content, color, dry matter, texture properties, and the count of lactic acid bacteria. In all samples, similar growth of LAB was observed. Significant degradation of chlorophylls into pheophytins was observed after the fermentation process. No significant differences were observed in the parameters tested, depending on the addition of dedicated LAB strains. After the fermentation process, the vitamin C and total polyphenols content is what influenced the antioxidant activity of the samples. It can be stated that the fermentation process changed the red bell pepper samples in the smallest way and the green ones in the highest way.