Personalized and self-initiated dietary adjustments have been shown to alleviate mental and somatic complaints. Here, we investigated the potential role of gut microbiome alterations underlying these effects. For this purpose, participants (n = 185) underwent a four-week self-initiated dietary intervention and filled out weekly questionnaires on their dietary intake, somatic and mental symptoms, and physical activity. Overall, the participants lost weight, had alleviated mental and somatic complaints, reduced their total caloric and percentual carbohydrate intake, and ate less processed, party-type, and traditional Dutch food items, but ate more Pescatarian type food items, while keeping their fiber intake unaltered. Baseline and endpoint gut microbiota analyses using 16S rRNA gene sequencing revealed an overall increase in and reductions in and over the four-week dietary intervention. While these bacterial alterations were considered to be beneficial for the host, they were not individually correlated with alterations in, or endpoint levels of, somatic and/or mental complaints. Instead, individual increases in (a well-known utilizer of plant cell wall polysaccharides) were strongly correlated with reductions in mental complaints, even though overall remained unaltered over the course of the four-week self-initiated dierary intervention. Our results suggest that overall altered versus individually correlated microbiota abundances and their relations with host health characteristics over the course of a self-chosen dietary intervention may represent different levels of regulation, which remain to be further untangled.