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This study aims at assessing selected factors affecting performance appraisal in the Presbyterian Church of East Africa, a case study in Central Region. The researcher based the study on the following objectives: To examine how training affects performance appraisal in church-based organizations in Kenya; To find out how working conditions affect performance appraisal in Church-based organizations in Kenya; To assess the effect of employee attitude on performance appraisal in church based organizations in Kenya; To find out the effect workload has on performance appraisal in church based organization in Kenya. Performance appraisal is a crucial tool in HRM for use in all kinds of Organisations, whether profit making or nonprofit making, private or public, religious or secular and small or large. There has been a dilemma whether performance appraisal is necessary in Church based Organisations which have its human resource drawn mainly from clergy and volunteers who believe that their service is mainly driven by faith and not by supervision or evaluations from earthly masters. For church based organisation which conduct Performance appraisal there are factors which affect the system, In this Study the Researcher selected four of this factors. A Descriptive Survey approach was used in the investigation.The descriptive survey method was utilized in this case since the study is based on the state of conditions as they are in the field, and no variables were changed. The researcher used stratified and purposive random sample approaches to get credible key informants. The total number interviewed were 84 respondents, including: 21 Ministers, 21, Pairing elders, 21 Evangelists 21 Secretaries. Data was subsequently evaluated utilizing descriptive analysis techniques. Frequencies, percentages, summing ratings, and Mean are among the descriptive analysis approaches. To evaluate the data and exhibit it in tables and charts, computer-based quantitative data products (SPSS Version 22.0) were employed. To analyse qualitative data, the content analysis method was applied. The Nvivo 8 computer suite was used to analyse all data acquired from Focused Group Discussions or In-depth Interviews. The researcher also used the Statistical Package for Social Sciences (SPSS) version 22.0. In the Study it has been observed that P.C.E.A embraces performance appraisal and in its GAC of 2013 the Business committee which runs the Church from one General Assembly to the other ,it was instructed to ensure that there is use of current management skills to ensure formulation and implementation of church programmes.The church since the time has been having the practice of performance appraisal in some of its parishes and presbyteries. The results in the study show that; on how training affect Performance Appraisal and to what extent, majority of the respondents indicated it is great at 60% while 40% showed it was greater. Effect of Working condition has 80% indicating it is Greater and 20% responding it is great. On extent of effect of attitude,55%felt it is Greatest 27%Greater and 18% great. Finally on the extent of effect of Workload, 37% responded it is greater at 37% and 63% responding it is great. It is therefore evident from this Study that Training,working condition, employee attitude has a significant effect to Performance appraisal. The study recommend Training of both the Appraisee and appraiser before the Appraisal exercise and establish systems that promote attitude, while improving on the working Conditions and ensuring the right Workload.