The Balkan pepper breeding program aims to use in vitro embryogenesis (anther culture) to develop doubled haploid pepper lines with valuable traits. We analyzed the effectiveness of microspore embryogenesis on 17 pepper genotypes comprised of varieties, breeding lines, and F1 hybrids of different varietal types (conical, bell shape, and kapia) and characterized the agronomic traits of newly generated doubled haploid lines. The highest androgenic potential was observed in the variety Stryama and breeding line 560/06 with 9.55 and 13.00% reacted anthers, respectively. Of the 186 regenerated plants, 147 were successfully adapted with a survival index of 79.03%. Flow cytometry analysis showed that the haploid:diploid ratio of regenerants was 1.5:1. All diploid plants were confirmed to be androgenic in origin. There were significant differences in terms of quantitative fruit characteristics of length, width, weight, pericarp weight, pericarp thickness, and productivity per plant among the diploid lines. Also, androgenic lines 21, 23, and 74 derived from Stryama and line 55 obtained from Zlaten medal 7 were distinguished with higher values of some fruit traits compared to initial genotypes. Additionally, several androgenesis lines (Stryama lines 21, 23, and 74, and Zlaten medal 7 line 55) scored higher for some fruit traits compared to the initial genotype. These results show that anther culture is a promising tool for the creation of Balkan pepper breeding lines with improved traits.