During the past 40 years, the US fresh-cut product market has experienced a consistent increase in demand because consumers prioritize health and convenience. Increased interest in fresh-cut products and ready-to-eat vegetables has led to innovations in breeding, product selection, and packaging. However, despite the increased popularity of bell pepper and chile pepper (Capsicum annuum L.), research of fresh-cut jalapeño pepper is limited. This study was conducted to identify jalapeño cultivars that could be suitable as a raw fresh-cut product and explore measures beyond tissue membrane electrolyte leakage (EL) of processed products that may be useful for the identification of cultivars suitable for fresh-cut applications. A total of 22 fresh-cut parameters were examined across five cultivars of jalapeño peppers and 10 intercrosses of these cultivars, including visual quality based on an image analysis via a computer vision system, package headspace gas composition, tissue membrane EL, and texture. Based on our results, the genotypes were grouped into five clusters using a cluster analysis. Variables including tissue softening (r2 = 0.95), EL (r2 = 0.95), total energy of the mesocarp (r2 = 0.95), and package headspace carbon dioxide (CO2) partial pressure (r2 = 0.94) had strong associations with the cluster. A principal component analysis with biplots further confirmed the results. Cultivars Goliath and Emerald Fire and their hybrids in the first and second clusters showed good quality for fresh-cut applications. The fifth cluster, represented by a single cultivar, Jalapeño M, had the smallest physical size, rapid shelf-life decline, accumulated CO2 partial pressures, increased EL, and rapid tissue softening in comparison with the other genotypes. All jalapeño cultivars except Jalapeño M maintained good quality until day 14 postprocessing, and some maintained good quality until 21 days postprocessing. Hybrid crosses suggested that two of the cultivars evaluated, Goliath and Emerald Fire, were useful as parents when transferring superior fresh-cut quality traits to progeny. Traditionally, the EL level has been used as an index of freshness (or tissue deterioration). Our results showed that other quality analyses, including measurements of tissue softening via an imaging analysis, and physical analyses of tissue firmness can also be used as indices for the freshness of fresh-cut jalapeños. The results suggest that fruit size, wall thickness, and skin toughness might be useful as predictive measures in the field for the selection of jalapeño genotypes with superior fresh-cut quality.