The aims of this research were to evaluate the influence of intermittent microwave drying on the moisture diffusion and color qualities of organically and conventionally grown sweet red peppers and mathematically express drying kinetic data. Pepper samples of 150 g were dried at 150, 300 and 450 W using a microwave oven. Results showed that intermittent microwave drying at 450 W occurred mainly in the falling rate period, whereas drying at lower powers resulted in relatively longer constant rate periods for both peppers types. The Midilli model provided the best fit for all data. The moisture diffusivity (D_eff) values of organic and conventional samples ranged from 59.69 × 10⁻¹⁰ to 182.01 × 10⁻¹⁰ m²s⁻¹ and from 59.11 × 10⁻¹⁰ to 181.01 × 10⁻¹⁰ m²s⁻¹, respectively, and the difference was insignificant. The pre-exponential factor for the Arrhenius equation (D₀) and activation energy (E_a) values were almost identical for both product types. Overall, organic or conventional growing did not alter the structural features related to the heat transfer properties. Intermittent microwave drying at 150 and 300 W for organic peppers and 150 W for conventional peppers gave the highest ΔL*, Δa* and a*/b* values, producing the most bright and red pepper powders. Thus, these treatments can be used to produce higher color quality powders.