In 1931-32, the MKT constructed a new lift-span bridge across the Missouri River at Boonville, including a new girder span over the MoPac mainline on the south bank of the river. The original bridge, though an impressive sight in itself, had not been constructed to handle the heavier modern railroad equipment and was beginning to deteriorate under the loads. At the time of its completion, the new bridge had the longest railroad lift-span bridge in the world.

The years of the Great Depression brought years of decay for the line. In 1933, passenger service between Parsons and St. Louis was reduced to one train a day each way, provided by the "Katy Flyer". However, World War II brought much-needed prosperity for the MKT- and the railroad industry as a whole. But after the war, the traffic began to dry up to pre-war levels and Katy returned to a status of decline. In order to trim operating costs, the MKT implemented cost cutting measures which included the abandonment of many miles of secondary and branchlines and the discontinuance of the Katy Flyer passenger train on April 30, 1958 (in 1965, the last MKT passenger run from Kansas City to San Antonio was finally axed). Also in the late 1950's, the Walker-Eldorado Springs branch was dismantled, and in 1958, the Bryson, MO to Paola, KS branch saw its last train and was abandoned.