He contributed articles to Stanislav Kostka Neumann's Června, Bedřich Václavek's Studentské revue, and worked with Zdeněk Nejedlý on the magazine Var.

In February 1948, he demonstratively rejoined the Communist Party of Czechoslovakia and became a high functionary in the regional action committee.

At the National Culture Congress in April 1948, he spoke of the necessity of "subordinating the freedom of academic research to the emerging political situations".

[6] Nevertheless, at the close of 1948 he resigned from political functions, and in 1954 he wrote and sent a memorandum to the highest party and state authorities in which he criticised educational reform (including a protest against the closing of the Palacký University Faculty Arts and its transformation into the Faculty of Social Sciences of the newly established Higher School of Education).

Because no suitable position was found for Fischer at the "expiring" Faculty of Arts, in May 1956, he was transferred to the Teacher Training University in Olomouc.

[7] When more liberal conditions prevailed in the second half of the 1960s, Fischer took advantage of this to publish in professional journals, and in 1965 he briefly worked at the Department of Psychology in the reinstated Palacký University Faculty of Arts.

However, during the Normalization period, he was retired (1970), and the second edition of Sokrates nelegendární, prepared for publication in 1970, was not published due to political reasons.

In accordance with his conviction of the permanent incompleteness of our knowledge, he continued to rethink his categorical system and studied new natural science material for a planned contribution to the Soviet journal Voprosy filosofii (Questions of Philosophy).

Since 1994, a bronze memorial plaque with a relief of J. L. Fischer has been placed in the vestibule of the Palacký University Rector's Office.

He saw a way out of the crisis in the ontological rehabilitation of quality, which he returned to elaborate, along with other categories of function and structure, in his collection Filosofických studií (Philosophical Studies, 1968).

Zdeněk Vašíček recalled: "Ludvík Svoboda [President of Czechoslovakia 1968–1975] (...) in his memoirs [Cestami života, Vol 1, 1971] declares his deep interest in JLF in the 1930s and devotes a good twenty pages to the contents of his book ‘Krize demokracie’ [Crisis of Democracy].