As a young man he read the writings of the anarchist social critic Pierre-Joseph Proudhon, which greatly influenced him.

As a firm believer in the equality of the sexes, he promoted the anarchist and feminist Nathalie Lemel (1827–1921) to a leading position in the bank.

Varlin believed that the nascent trade unions should overcome their professional, local and national particularism and form a united international labour movement, dedicated, as the statutes of his bookbinders' union put it, "to the constant improvement of the conditions of existence of ... the workers of all professions and all countries, and to [bringing] workers into possession of the instruments of their labour.

Trade unions were not fully legal, and the International was treated as a dangerous conspiracy, so Varlin was arrested numerous times.

In 1870, he helped organise protests against the impending war between France and Prussia and co-authored the anti-war manifesto of the Parisian section of the International.

During the siege of Paris by the Prussians, Varlin devoted himself to organising relief for the population; his care packages became known as 'Varlin's marmites' (named after his co-operative restaurant).

On 26 March he was elected by a landslide to the Council of the Paris Commune, representing the sixth, twelfth and seventeenth arrondissements (districts).

Among the various political factions which participated in the Paris Commune, Varlin sided with the Proudhonists, belonging to the left wing of that group.

Varlin participated actively in the fighting against the troops of the Versailles government and was in charge of the defence of the sixth and eleventh arrondissements.