Despite all the works of the foreign missions in Kerala, there is a few negative sides to their ministry in Kerala. The following short comings can be observed about the work of foreign missionaries in Kerala and India.
Many people accepted the faith to escape form the social evils and to raise their standard of living. The people noticed that the new converts found it easier to get education and jobs at the missionary establishments. So people got converted in order to get the physical and financial benefits of being a christian without any change of the heart. This latter on lead to the labeling of many christians as 'Rice Christians' because the missionaries gave food to the starving converts and many got converted to get the food.
The missionaries could not succeed in establishing a new culture. They adapted the local culture after making some essential changes. The lack of a Judeo-Christian culture becomes very apparent at the present efforts to evangalise Kerala.
Some missionaries spent almost all their time and energy for education and social reformation instead of preaching the Gospel. Although it was a great assert to the missionaries who came later, their work was limited.
Along with the Bible and christian books the missionaries printed some Hindu literature also. This helped to spread the Hindu theology and philosophy which was later used to stop the growth of Christianity. It is doubtful whether such open-mindedness was really necessary among the missionaries who was here in the purpose of propagating Christanity.
The missionaries were not successful in making disciples capable of continuing their work. Such local leaders were rare in Kerala history. Although there are people like K V Simon, Sadhu Kochu Kunju Upadesi, etc. the vast majority of the people were followers rather than leaders. The lack of leaders was a serious limitations to further mission programs.
The Missionaries concentrated in converting the lower class people. The ignored upper class people were a hindrance to future missions. Christanity was also labeled as a religion of the lower class in many parts of India due to this reason.
The Missionaries naturally supported the British rule in India. Due to this the new converts were labeled unpatriotic and anti-Indian. This caused many troubles in the spread of Gospel in the independent India.
Many conversion were not true. For example when Raja Jacob Ramavarma became a Christian there were many conversions. A quarter of Travancor became Christians by 1910. But there is a positive aspect to this. The next generation of these christians had many people who were truly converted.