Process innovation is an important topic in business research. It enables competitive advantages for companies if managed properly. It is previously acknowledged that uncertainty in process innovation is common and previously research show that it has a negative impact on process innovation projects, as it can cause a waste of resources for the company. For SME’s, where resources are limited, it is imperative that uncertainty do not affect process innovation projects negatively. Previous scholars do not identify sources of process innovation uncertainty in SME’s or how it can be managed, thus leave a gap in theory that is important to fill. The purpose of the study was to investigate how uncertainty in process innovation arises in an SME and how it can be reduced by an investigation on how SEO, as an instance of process innovation, was perceived before and after an implementation process and if a change in perception was related to uncertainty. A single case study with qualitative interviews, combined with an implementation process of SEO, was used to investigate the topic and generate in-depth knowledge. Our findings identify sources of process innovation uncertainty in SME’s, arising from either a resource perspective or from an organizational perspective. Furthermore, we suggest how to manage the identified sources of uncertainty through either information, communication or results. Organizations can use these findings to manage process innovation uncertainty before it arises, thus achieve successful process innovation.