Simple Summary Looking for non-antibiotic substances that can enhance health by improving the gastrointestinal microbiome of animals is an ongoing task. Among other compounds, medium-chain fatty acids, such as lauric acid, can exert positive effects. Coconut oil is a rich source of lauric acid, and therefore, the aim of this study was to describe the effect of adding coconut oil to the feed of growing pigs on intestinal microbiome diversity and bacterial abundance. Rectal swab samples were analyzed to assess the intestinal microbiomes of pigs. Typically, growing pigs are characterized by continuously changing bacterial communities as a result of aging. However, a significant effect of coconut oil treatment was detected in the presented study. Decreases in Corynebacterium , Pseudomonadales , and Mitsuokella and increases in Alloprevotella , Bifidobacteriales , and Lactobacilli could be attributed to the supplementation of feed with coconut oil. Coconut oil treatment did not have a significant effect on the diversity index of rectal microbiomes, but an abundant increase in probiotics such as Bifidobacterium and Lactobacillus in the gastrointestinal tract is desirable in pig breeding. From this point of view, the addition of coconut oil to the feed of pigs is a good option for improving the microbiome in their gastrointestinal tracts. Abstract Coconut oil has a high content of lauric acid, which has selective antibacterial activity. This study aimed to explore the effect of coconut oil ingestion on the gastrointestinal microbiomes of pigs. A 14-day-long feeding experiment included 19 pigs in two groups (9 on a normal diet and 10 on a diet supplemented with coconut oil). At the start and end of the experiment, a rectal swab sample was taken from each pig in both groups, and total bacterial DNA was extracted. We used 16S r RNA high-throughput amplicon sequencing to evaluate the microbiome changes during the feeding experiment. A total of 446 operational taxonomic units (OTUs) were detected in the whole sample set. Shannon’s indices of bacterial diversity did not change significantly during the experiment. Changes in the bacterial community during the study period and in response to the coconut oil treatment were highly significant ( p < 0.001). During the study, an increase in the abundance of Lactobacillus was detected in the group treated with coconut oil. An increase in Alloprevotella, Bifidobacteriales , and Lactobacillales and a decrease in Corynebacterium , Mitsuokella, Psychrobacter , and Pseudomonadales were attributed to the coconut oil treatment. Although the addition of coconut oil to pig feed did not affect Shannon’s index of diversity, it had a positive effect on the abundance of bacterial groups that are considered to be commensal and/or probiotic.