On September 20, 2018, about 1830 UTC, a Berry Aviation Inc. Embraer EMB-120ER, N233SW, found substantial damage to the cargo area after arriving at Queretaro International Airport (MMQT), Queretaro, Mexico. The two flight crew members were not injured. The flight was being operated as a 14 Code of Federal Regulations Part 135 international cargo flight from Shreveport Regional Airport (KSHV), Shreveport, Louisiana, to MMQT. While in cruise flight in Houston, Texas, airspace, the flight crew noticed a storm cell on the weather radar, however, they continued on their routing since they would stay south of the storm. While passing the storm, they encountered severe turbulence for a short period of time. The flight crew notified ATC of the location of the severe turbulence and continued the flight. Upon arrival at MMQT, the flight crew entered the cargo area where they noticed several panels had fallen and were hanging from their attachment points. Further maintenance inspection revealed buckling to four fuselage frames and four floor support structures that covered an area several feet long. The damage was classified as substantial as it would adversely affect the structural strength of the fuselage. The flight crew reported they picked up four pallets of cargo at John C. Munro Hamilton International Airport (CYHM), Hamilton, Ontario, Canada. Two of the pallets were loaded in zone 2 and two were loaded into zone 3. The pallets were secured with vertical cargo nets. The flight crew departed CYHM at 1322 UTC and arrived at KSHV at 1657 to clear US customs and to take on fuel. They departed KSHV at 1727 UTC for MMQT. After the accident, the operator reminded flight crews to fly 5 or more miles away from thunderstorm cells identified on the weather radar and to secure cargo better to decrease the likelihood that it will shift during turbulence encounters.