The objective of this pilot study was to assess the fecal microbiome and different immunological parameters in infant feces and maternal milk from mother–infant pairs in which the infants were suffering from different gastrointestinal disorders (colic, non-IgE-mediated cow milk protein allergy (CMPA), and proctocolitis). A cohort of 30 mother–infant pairs, in which the infants were diagnosed with these gastrointestinal disorders or included as healthy controls, were recruited. Bacterial composition of infant feces and breast milk was determined by metataxonomic sequencing. Immunological compounds were quantified using multiplexed immunoassays. A higher abundance of Eggerthellaceae, Lachnospiraceae and Peptostreptococcaceae, and lower abundance of Bifidobacterium and higher abundance of Rothia were registered in fecal samples from the CMPA group. Eggerthellaceae was also significantly more abundant in milk samples of the CMPA group. There were no differences in the concentration of immunological compounds in infant fecal samples between the four groups. In contrast, differences were found in the concentration and/or frequency of compounds related to acquired immunity and granulocyte colony stimulating factor (GCSF) in breast milk samples. In conclusion, a few microbial signatures in feces may explain part of the difference between CMPA and other infants. In addition, some milk immunological signatures have been uncovered among the different conditions addressed in this pilot study.