Zachwatowicz was born in Gatchina. He studied Industrial Civil Engineering at the Saint Petersburg Polytechnical University, and graduated from the School of Architecture at the Warsaw University of Technology in 1930. He was awarded with the SARP Honorary Award (1971; Polish: Honorowa Nagroda Stowarzyszenie Architektów Polskich).
He was a professor of the Warsaw University of Technology (since 1946; he worked there since 1925), member of the Polish Academy of Sciences (since 1952), member of the Académie d'architecture in Paris (since 1967), member of the International Council on Monuments and Sites, general restorer of relics in Poland (from 1945 to 1957; Polish: Generalny Konserwator Zabytków), chairman of the Architectural-Restoration Committee (since 1971; Polish: Komisja Architektoniczno-Konserwatorska), and chairman of the Civil Committee of Royal Castle in Warsaw Reconstruction (Polish: Obywatelski Komitet Odbudowy Zamku Królewskiego w Warszawie).
Zachwatowicz contributed to reorganization and enlargement of Polish restoration service. During the occupation of Poland (1939–1945) he took a part of teaching, protecting and saving works, i.e. set of relic buildings measurements (including The Market Square of Warsaw Old Town). From January 1945 he co-directed the Warsaw Reconstruction Office (Polish: Biuro Odbudowy Stolicy; f. Biuro Organizacji Odbudowy Warszawy).
After World War II, many other historic buildings in Gdańsk, Poznań, and Wrocław were restored or rebuilt according to principles established by Zachwatowicz and his team. Among his many achievements was the rebuilding of St. John's Cathedral, Warsaw (1960).
He was a scholar with over 200 major publications to his credit.
- Ochrona Zabytków w Polsce (1965)
- Architektura polska (1966)
- Sztuka polska przedromańska i romańska do schyłku XIII wieku (1971; collective work)
- Zamek Królewski w Warszawie (1972)
- "Zachwatowicz Jan". Internetowa encyklopedia PWN (in Polish). Retrieved 2007-05-12.
- "Zachawa Boris Jewgienjewicz". WIEM Encyclopedia (in Polish). Retrieved 2007-05-12.
- "Jan Zachwatowicz". Album przedwojennej Warszawy (in Polish). Retrieved 2007-05-12.
- "Honorowa Nagroda SARP" (in Polish). 2005-12-02. Archived from the original on 2004-01-06. Retrieved 2007-05-12.
- Testimony of Jan Zachwatowicz about German policy in occupied Warsaw - Chronicles of Terror collection