The effect of pressure treatments of 100 and 200 MPa (10 and 20 min) and of thermal blanching at 70 °C, 80 °C and 98 °C (1 and 2.5 min), on sweet green and red bell peppers was compared. Pressure treated peppers showed a lower reduction on soluble protein and ascorbic acid contents. Red peppers presented even an increased content of ascorbic acid (15–20%), compared to the untreated peppers. Peroxidase and pectin methylesterase (whose activity was only quantifiable in green peppers) showed a higher stability to pressure treatments, particularly the latter enzyme, while polyphenol oxidase was inactivated to the same final level by the thermal blanching and pressure treatments. Pressure treatments resulted in comparable (in green pepper) to higher (in red pepper) microbial loads compared to blanching. Pressure treated green and red peppers presented similar to better firmness before and after tunnel freezing at −30 °C, compared to thermally blanched peppers, particularly those blanched at 98 °C. The results indicated that pressure treatments of 100 and 200 MPa can be used to produce frozen peppers with similar to better nutritional (soluble protein and ascorbic acid) and texture (firmness) characteristics, comparable activity of polyphenol oxidase and higher activity of pectin methylesterase, while pressure treated peppers show a higher level of peroxidase activity. It would be interesting to use higher pressures in future studies, as an attempt to cause a higher reduction on microbial load and on enzymatic activity.