Jaffna was a busy trading city and the main centre in northern Ceylon. The last bastion of the Portuguese on the island, it fell to the Company in 1658. For the time being the VOC had eliminated all its European competitors on the island. The Company rebuilt much of Jaffna. The Portuguese fort made way for a new one designed according to the latest military principles. The result was an almost impregnable citadel, perhaps the strongest VOC fort in Asia. Construction work, which began in 1660, was finally completed some 130 years later, in 1792. The fort was an important link, guarding the sea lanes to and from India. In Jaffna fort the VOC built a church, known as 'Kruys' (Cross) church. With its layout in the form of a Greek cross, it was typical of Calvinist architecture. Women attending the church services would have their slaves bring chairs which would be taken away again afterwards. The church was built in 1706 and could accommodate 600 people. In the Jaffna region, too, Protestantism was preached with enthusiasm, but the native population often had little idea of the difference between Protestantism and Catholicism. In the busy trading town of Jaffna the merchants maintained close contacts with the mainland. The main products of the town and region were cotton, clothes, pearls and elephants. The elephants were sold for the armies of Indian princes. The animals were captured by driving them into a fenced enclosure from where they were taken one by one to be bound and even sometimes to be baptised. After eight days of being tied up an elephant would be more or less tame and ready to be trained. In northern Ceylon the Company enjoyed a certain measure of territorial authority; a unique position for an organisation primarily concerned with trade which (except on Formosa) generally left local rulers in control. On Ceylon this authority involved the Company was responsible for collecting taxes from the local population, among other things. Because the Company levied far higher taxes than was customary, the local inhabitants rose up against the VOC in 1676. However the Company crushed the rebellion and implemented the levy anyway. Jaffna was also the capital of one of the 'commandementen', or departments, into which Ceylon was divided and fell under the jurisdiction of the governor in Colombo.
Jaffna ilikuwa jiji lenye shughuli nyingi za kibiashara na kituo kikuu cha kaskazini mwa Ceylon. Ngome ya mwisho ya Ureno katika kisiwa hicho ilianguka kwa Kampuni hiyo mwaka 1658. Kwa wakati huo VOC ilikuwa imeondoa washindani wake wote wa Ulaya katika kisiwa hicho. Kampuni hiyo ilijenga upya sehemu kubwa ya Jaffna. Ngome ya Kireno ilifanyizwa kwa ajili ya ngome mpya iliyojengwa kulingana na kanuni za kisasa za kijeshi. Matokeo yakawa ngome ambayo haingeweza kushambuliwa, labda ngome yenye nguvu zaidi ya VOC katika Asia. Kazi ya ujenzi ilianza mwaka wa 1660 na kukamilika mwaka wa 1792. Ngome hiyo ilikuwa kiungo muhimu, ikilinda njia za baharini za kwenda na kutoka India. Katika ngome ya Jaffna VOC ilijenga kanisa, linalojulikana kama 'Kruys' (Msalaba) kanisa. Jengo hilo lilijengwa kwa umbo la msalaba wa Kigiriki, na lilikuwa la kawaida katika usanifu-ujenzi wa Wakalvini. Wanawake waliohudhuria ibada za kanisa waliwaomba watumwa wao walete viti ambavyo vilikuwa vimechukuliwa tena baadaye. Kanisa hilo lilijengwa mwaka wa 1706 na lilikuwa na nafasi ya watu 600. Katika eneo la Jaffna, pia, Uprotestanti ulihubiriwa kwa shauku, lakini mara nyingi wenyeji walikuwa na wazo dogo la tofauti kati ya Uprotestanti na Ukatoliki. Katika mji wenye shughuli nyingi wa biashara wa Jaffna wafanyabiashara waliendelea kuwasiliana kwa ukaribu na bara. Bidhaa kuu za mji na eneo hilo zilikuwa pamba, nguo, lulu na tembo. Tembo hao waliuzwa kwa ajili ya majeshi ya wakuu wa India. Wanyama hao walipelekwa kwenye gereza lililokuwa na uzio, na mmoja baada ya mwingine akafungwa na hata wakati mwingine akabatizwa. Baada ya siku nane za kufungwa, tembo angekuwa amezaa na tayari kuzoezwa. Katika kaskazini mwa Ceylon, Kampuni hiyo ilikuwa na mamlaka ya eneo fulani, nafasi ya kipekee kwa shirika lililohusika hasa na biashara ambayo ( isipokuwa Formosa) kwa ujumla iliwaacha watawala wa eneo hilo wakidhibiti. Katika Ceylon mamlaka hii ilihusisha Kampuni ilikuwa na jukumu la kukusanya kodi kutoka kwa idadi ya watu wa eneo hilo, miongoni mwa mambo mengine. Kwa sababu Kampuni hiyo ilitoza kodi kubwa kuliko ilivyokuwa desturi, wakazi wa eneo hilo waliasi dhidi ya VOC mwaka wa 1676. Hata hivyo Kampuni ilikandamiza uasi huo na kutekeleza ushuru huo hata hivyo. Jaffna pia ilikuwa mji mkuu wa moja ya 'commandementen', au idara, ambayo Ceylon iligawanywa na kuanguka chini ya mamlaka ya gavana katika Colombo.