The aim of this study was to determine the effect of temperature and CO2 on seed emergence, seedling quality, and phenological stage of Capsicum chinense and Capsicum annum cultivated in four controlled growth chambers (C1: 30 °C and 400 μmol CO2 mol−1; C2: 40 °C and 1200 μmol CO2 mol−1; C3: 30 °C and 1200 μmol CO2 mol−1; C4: 40 °C and 400 μmol CO2 mol−1). Neither temperature nor elevated CO2 influenced seed emergence, although differences were observed in seedling mortality, with high temperature affecting seedling survival in both species; the mortality rate at 40 °C was 20 and 53% in C. annuum and 45 and 58% in C. chinense at 400 and 1200 μmol CO2 mol−1, respectively. Differences were also observed in growth parameters, where positive effects were observed on leaf area, which reached 45.9 cm2 in C. annuum and 23.9 cm2 in C. chinense with elevated CO2 at 30 °C, but negative effects were observed with high temperature. CO2 enrichment increased flower and fruit production per plant. However, high temperature delayed flower phenology, increased flower abortion and inhibited fruit set. Elevated CO2 counteracted the detrimental effects of high temperature on growth parameters and flower number, but this was not sufficient to prevent flower abortion and the detrimental morphological characteristics of fruit caused by a temperature of 40 °C.