<p>This experimental study aimed to determine the effect of psycho-pedagogical intervention on spiritual intelligence, happiness, and spiritual well-being of primary school students in Latvia. Three measurements (pre-intervention, post-intervention, and three month follow up) were administered for 83 children (<i>n</i> = 41 experimental group; <i>n</i> = 42 control group). The experimental group participated in intervention sessions that met once per week for 10 weeks. The results indicated that participation in the intervention programme led to a statistically significant increase in spiritual intelligence, happiness, and spiritual well-being in the experimental group compared to the control group. The intervention had the most significant effect on spiritual intelligence and spiritual well-being. Gender differences in spiritual intelligence, spiritual well-being, and happiness were softened after the intervention. The effectiveness of the intervention was consistent between all participants in the experimental group, regardless of the frequency of church attendance. Children who occasionally attended church showed slightly higher improvements in both groups, although not statistically significant. The given study not only validated the effect of the designed programme for primary school students, but also showed that the given intervention can improve spiritual intelligence, happiness and spiritual well-being irrespective of gender or church attendance. Integrating spiritual development into the primary school curriculum nurtures a harmonious and mentally healthy personality, which is one of the main goals of education.</p>