Background: Numerous scientific studies on patients with autism spectrum disorder (ASD) suggest a significant role of inflammation processes or lipid disorders in this spectrum of neurodevelopmental disorders. Unfortunately, there is a lack of assessments of changes over time regarding level of lipids and inflammatory markers in people diagnosed with ASD using different diets. The aim of this study was to evaluate changes in lipid profile, high sensitivity C-reactive protein (hs-CRP) and body mass index (BMI) in individuals diagnosed with ASD and healthy controls. Variables were assessed at two time points (2015/17 and 2017/20) for each subject. Methods: After applying the selection criteria, for the first assessment period, 96 participants were qualified (the group consisted of 59 males with ASD and 37 healthy volunteers, i.e., age-matched control group—CG). The final assessment included 93 participants (57 from ASD group and 36 from CG). Subjects were on low-fat diet (LFD), gluten–casein-free diet (GF–CF) and regular diet (RD), respectively. All members of CG were on regular diet. A fasting lipid profile and hs-CRP level were analyzed. BMI and percentiles were calculated. Eating habits were checked by analyzing data from questionnaires. Principal component analysis (PCA) was used separately for every assessment. The Mann–Whitney U test was used to compare the medians of variables in the scheme of pairwise comparisons between control and ASD groups on different diets for separate assessment, while differences over time between variables were tested by Wilcoxon signed-rank test. Results: Statistically significant differences between BMI, CRP, triglycerides (TG), total cholesterol (TC), high-density lipoprotein (HDL), non-HDL-C and TC/HDL ratio were found in ASD group in comparison to healthy volunteers (increased BMI, CRP and TC/HDL and decreased HDL-C for all types of diets, increased TG in the group of LFD and RD individual and increased non-HDL-C in the group of GF–CF and RD individuals) during the first assessment period. The second assessment over time also showed increased levels of TC, non HDL-C and TC/HDL and decreased level of HDL-C for all ASD individuals regardless of diets used, while BMI and CRP increased only for individuals on LFD and RD. No statistically significant correlations between age of participants and other variables comparing with CG were found. Conclusions: Our studies suggest that targeted, individualized nutritional pattern and periodic screening for lipid and immune disorders would be beneficial for teenagers and adults diagnosed with ASD.