After his release, he worked in a number of magazines, including Дело (Cause), Записки Сибирского отдела РГО (Notes of the Siberian Department of the Russian Geographic Society), and others.

Afanasiy Shchapov authored many works on the history of sectarianism and Raskol, which he viewed as a manifestation of popular protest against social oppression.

In 1856-1864, influenced by Grigory Yeliseyev and Stepan Yeshevsky, he came forward as a supporter of the so-called "zemstvo-oblast theory" (земско-областническая теория), viewing Russian history as an interaction process between certain "oblasts".

Shchapov's focus on geography and economics as two principal agencies in history is thought to have heralded the next generation of Russian historians, as represented by Vasily Klyuchevsky, Paul Vinogradoff, and Michael Rostovtzeff.

He held that Sibiryaks were ethnically distinct from the rest of Russian nation, as their character was shaped by rugged nature of inhospitable land they lived in and by the adventurous and enterprising spirit of the Old Believers who had been the original settlers of Siberia.