Although the California Zephyr performed well enough from a financial point of view during the 1950s and most of the 1960s, by 1966 the economics had deteriorated enough that Western Pacific, the weakest of its three operating partners, sought to discontinue its portion of the train. Public outcry was immediate and vocal, and the Interstate Commerce Commission balked, calling the train a "unique national asset". Unfortunately, though, public outcry did not translate into financial return, and an increasingly desperate Western Pacific was finally given its release to discontinue passenger service in March 1970. However, the I. C. C. mandated that some vestige of California Zephyr service had to continue. Burlington and Rio Grande eventually won I. C. C. approval for this train, which would offer tri-weekly service over the old CZ route between Denver and Salt Lake City with the train continuing north to Ogden where passengers could make a cross-platform transfer to Southern Pacific's City of San Francisco...by then itself a tri-weekly train. The last "real" California Zephyrs left the terminals of Oakland and Chicago on March 20, 1970, 21 years to the day after their inaugural runs, each arriving two days later on March 22, with this restructured "California Service/Rio Grande Zephyr" picking up after that date.

When Amtrak began operations in 1971 it originally intended to route its California service over this same itinerary. However, Amtrak and Rio Grande could not come to agreement on terms and at the last minute the decision was made to route Amtrak's San Francisco Zephyr via Burlington to Denver, Union Pacific to Ogden via Cheyenne/Borie, and Southern Pacific from thence to Oakland/San Francisco while Rio Grande would keep the Rio Grande Zephyr in operation as a tri-weekly day train from Denver to Salt Lake City. (It did continue to operate to Ogden for a short time after the switch, but by 1973 the train terminated in Salt Lake City with a limo transfer available to Ogden.) Shorn of its overnight connection to Chicago, the sleeping and baggage cars on the RGZ became redundant and were sold off.

Rio Grande would continue operating the train into 1983, making it the last long-distance train operated by a private concern in North America. In 1983, though, Rio Grande and Amtrak finally came to terms and Amtrak shifted its Chicago-San Francisco service to operate over Rio Grande's spectacularly scenic route under the name of the California Zephyr.