During the Spanish Civil War 1936-1939, Manén continued his concert activity with tours of Europe, performing mainly in France, Germany, England and Austria. During this period he also maintained an artistic relationship with the Stuttgart Radio and carried out several recording sessions destined for broadcasting: in March 1936 he recorded his own works with the pianist Hubert Giesen; in November and December 1937 he recorded works by Bach, Schubert and himself with the pianist Alfred Kuntzsch and he conducted his ballet Rosario la Tirana; and in April 1939, in addition to recording some works by Bach and Hubay with the pianist Georg Schmid, he conducted the Overture La vida es sueño and recorded the Concerto da camera op. A-24 for violin, string orchestra and harp. During the same time his made regular appearances at “Salle Pleyel” and “Salle Gaveau” in Paris and the French critics praised the "clarity, sobriety and charm" of his performances (Le Journal, 04-06-1938). In 1938 his opera Nerón y Acté was performed at the Helsinki Opera House, this time translated into Finnish.
Joan Manén was one of the first violinists to use a steel-bound E string on his instrument. Furthermore, the “Gebrüder Schuster house” in Markneukirchen produced a set of gold-plated strings with the thickness that Manén used and named the string set "Joan Manén violen saite".
Manén always felt a great fascination for the figure of Niccoló Paganini. He made six arrangements of works such as “Le Streghe” or “I Palpiti” harmonising the piano accompaniment very freely - and he also composed an original work for violin and orchestra based on Paginini’s “Capricho nº24”. He studied the character of Paganini extensively and even wrote the plot for a screenplay titled “El secreto de Paganini”. After several unsuccessful attempts to bring the play to the screen, the text was finally published in 1964 as part of a book titled Relatos de un violinista, a compilation of stories about the music written by him. Between 1938 and 1939 he carried out a series of investigations to locate the eventual grave where Paganini was buried before receiving his permanent space at the Parma cemetery. The legend had it that Paganini had been buried a few years on the French isle of Saint-Ferréol and after several investigations with the help of his friend, the publicist Alain Courtau, Manén was convinced that this rumour was true. To certify the hypothesis definitively, he travelled several times to the isle in search of the remains of the tomb. He finally managed to find a grave hidden in the undergrowth that confirmed, according to his research, that Paganini had been buried there. He registered his discovery with the Cannes City Council, a municipal commission titled "Souvenir de Paganini" was created, and the inauguration of a monument in his memory was scheduled for the 27th of May, 1940 - the exact centenary of the death of the famous violinist. Unfortunately, the tribute had to be cancelled due to the outbreak of the Second World War.
With the Spanish Civil War just finishing and the outbreak of World War II, Manén saw many of his performances cancelled. Faced with a Europe in raging war and a post-war Spain, he decided to move with his family to Estoril (Portugal). During 1940 his performance activity was minimal and instead he devoted time to the composition of new works such as the Concerto No. 3, Iberico for violin and orchestra. He also began writing Mis Experiencias, the first volume of his memoirs that he would publish four years later. On the 16th of November, 1940, a monographic benefit concert with his symphonic works took place at “Teatro da Trindade” in Lisbon, in aid of the victims of the October floods in Catalonia that had caused 350 victims that year. During the concert, Pedro Freitas Branco and Joan Manén both conducted the National Orchestra of Portugal and Manén’s young Portuguese student Leonor Alves da Sousa participated. A symphonic fragment from Don Juan, the new opera trilogy which Manén had spent many years working on, was published with the title Introducción y baile de la tarantula.
Despite his decision to avoid the war by living in Portugal, Manén decided to perform in Germany and Austria in 1941 and 1942. The concerts took place in Berlin, Salzburg and Linz, among other cities. Surprisingly, while much of Europe suffered a bloody war in which thousands of human lives were lost every day, cultural life and concert series were maintained in the German capital and we can find Manén announced on the same poster as artists like Claudio Arrau, Wilhelm Kempff or Vasa Prihoda, among others.
On the 9th and 12th of April, 1942, just one month after performing in Berlin with the “Städtisches Orchester” under the direction of Fritz Zauner, Manén performed at “Palau de la Música” in Barcelona, ??after a seven years absence. Two "Manén Concerts" took place with the Iberian Concert Orchestra and the participation of Enric Casals as conductor and the violinist Leonor Alves da Souza, premiering the Concerto No. 3 Iberico by Joan Manén. On the 24th of April, the “Berlin Philharmoniker Orchester” made an appearance at “Gran Teatre del Liceu” performing works by Beethoven, Schubert, Strauss, Wagner and Introducción y baile de la tarantula from the opera Don Juan by Manén. From that moment onwards, the violinist began to normalize his artistic activity in Spain and would live for a time between Estoril and Barcelona, although he did not establish himself definitively in Barcelona until 1945.