In 1896, when it had become clear that he would be spending a significant portion of his life in South Africa, Gandhi made a brief return to India in order to collect his wife and children. While there, he published a pamphlet on the plight of Indians in South Africa (known to history as the Green Pamphlet) and experienced the first taste of the popular adulation that his work would eventually win him. He had developed a reputation as a champion of the poorest laborers in Natal, and when he went to visit the Indian province of Madras, the region where most of the laborers had originated, cheering crowds and wild enthusiasm greeted him. But he had promised his South African friends that he would be gone only six months; accordingly, he packed up Kasturbai and his children and sailed from Bombay in December 1896.

Upon his return to South Africa, however, a riotous crowd of whites awaited him at Port Natal. Gandhi had developed a considerable reputation as a troublemaker, and they were determined that he should not be allowed to land. Considerable confusion also fueled their anger; many of the rioters mistakenly believed that a number of dark-skinned passengers were a large number of poor Indian immigrants that Gandhi had brought with him. However, Gandhi was saved and escorted to safety by the port's Police Superintendent and his wife–it would not be the first time that his ability to get along with Englishmen would serve him well. Meanwhile, the confusion over the "immigrants" was cleared up (they were mostly returning Indian residents of Natal), and Gandhi's standing in the local white community was actually improved as a result of the incident.

He was soon back to work at the Natal Indian Congress, but within three years the Boer War impeded his political progress. This conflict, fought between the British and the twin Boer Republics, had been a long time coming, and it ended–after three years of furious and often brutal fighting– with the absorption of the Transvaal and the Orange Free State into the Empire. During the war, Gandhi was able to find a way to merge his loyalty to Britain against the Boers with his ardent pacifism: he organized and led an Indian medical corps that served on the British side and conducted itself with great bravery at a number of battles, including Spion Kop in January of 1900.

The loyalty that led Gandhi to assist the British army in the Boer War, it should be noted, was no pro forma matter. Gandhi's views on the subject of empire would later alter dramatically, but at this point in his life, and indeed, until the 1920s, he was an ardent British patriot, and his pro-British stance resulted from much thought. The Empire, he felt, embodied the principles of equality and liberty that he believed in, and he regarded the racist policies of the South African states as an aberration, rather than a defining trait, of British rule. Indeed, he saw the Raj as benevolent rather than tyrannical; despite its flaws, he believed that the Empire had been good for India, and that the ideals of the British constitution merited the loyalty of all British subjects across the globe, white, black and Indian alike. The man who would later bring down white rule in India could still, at this point in his life, declare that he and his fellow Indians were "proud to be under the British Crown," believing that "England will prove India's deliverer."

The end of the Boer War, Gandhi hoped, would bring the establishment of true British justice throughout South Africa–and an opportunity for him to return, more or less permanently, to India. He left Natal for Bombay in 1901, but before he left, his friends in the Natal Indian Congress made him promise to return immediately if they needed him in their political efforts. It was a pledge that he would be soon called upon to fulfill.

One of Gandhi's principal motivations for his return to India was his desire to attend the 1901 meeting of the Indian National Congress. The Congress, upon which his own Natalese organization was modeled, had been founded in 1885 by an Englishman, in the hopes of creating a social and political forum for the westernized Indian upper class. It had no real political power, and tended to be pro-British–however, at this point, Gandhi was also pro-British, and he saw the Congress as the only national organization that could claim to speak for India. He attended the 1901 Congress in the hopes of seeing the passage of a resolution supporting the Indian population of South Africa, and his hope was realized, largely through the work of G.K. Gokhale, the most significant Indian politician of his day. Gokhale knew Gandhi from before his move to South Africa, and Gandhi stayed a month as a guest in his household, forging numerous connections that would serve him well later in life.

But his time in India was cut short by an urgent telegram summoning him back to South Africa. Since the end of the war, the British and Boers (now referred to as Afrikaners) had been restoring good relations, often at the expense of the Indian population. Now Joseph Chamberlain, Secretary of State for the Colonies, had come to South Africa to finish the peacemaking. Gandhi returned in time to present Chamberlain with a paper outlining Indian grievances, but the Secretary remained unsympathetic. Britain planned for South Africa to become a self-governing colony along the lines of Canada and Australia, leaving power in the hands of the local (white-ruled) government. If the Indians wished to stay in Africa at all, Chamberlain hinted, they had better "placate" the Afrikaners.

So Gandhi, his hopes of post-war improvements dashed, went back to work. He set up camp in the Transvaal this time, deciding that his countrymen needed him more in that recently conquered region, and began representing Indians who had fled the Transvaal during the war and were now being overcharged for re-entry passes. When authorities dispossessed Indian inhabitants of a shantytown in order to clear the area for development, Gandhi represented these Indians as well. Collecting a staff around him that included several young women from Europe, he began (in 1904) the publication of a magazine, Indian Opinion, that agitated for political liberty in South Africa. The magazine soon found a readership throughout the country, and, with Gandhi writing the editorials himself, became both a vehicle for his fame and a wide platform for his ideas.